Do you oscillate your diet along with your riding? Briefly
If on alternate days you cycle and rest, and your ride uses, say, 1200 calories, what's better, to eat 2600 calories daily (and then where does the deficit come from on the riding days?) or to alternate between 3200 and 2000 calories (and what kind of diet supplies you with 3200 without disturbing your digestive system?).
For the impatient, let me illustrate the question with a figure.

Not So Briefly
My cyclocomputer tells me that my ride used 1200 calories. I'm here not trying to determine whether the figure is accurate. I'm trying to better understand the appropriate diet for a workout that uses such a substantial fraction (or, for some, a multiple) of the basic daily caloric needs. The other question (how can we—or how does a cyclocomputer—determine the calories used given distances, altitudes, heart rate samples, and speeds) is a very interesting question, but it is not the subject of the present discussion.
Since going through what was most likely &quot;hitting the wall,&quot; I've been cautious to eat more, especially carbs.
During the ride I can get 350 or so calories from three small snacks.
Right after the ride I attempt to use this glycogen replenishment window and consume 170 g (about a third of a pasta package) to get ~550 calories heavy in carbs. With a sauce and fruits this after-the-ride lunch might add up to 800 calories, which is not too far from what an adult might need without a workout (assuming vaguely 400+800+800 for the three meals).
The purpose of this worked-out example is to illustrates the difficulty of attempting to reach 3200 calories in a day.
If I did this route daily, it would be simple enough. Rather than the daily ~2000, I'd aim to consume ~3200 calories daily.
But, in full humility, admiration, and respect for those who can climb three mountain ranges racing one day and still be expected to repeat the feat on the following day, I need a day to rest.
What do you do if you ride a day and rest the next? Is it more sensible to increase your caloric intake to, in this example, 2600 daily, or would you alternate between 3200 and 2000?
I am not trying to lose weight. More importantly, I'm hoping to avoid that the caloric deficit would come from losing muscles.
If you choose option 1 (a regular diet), where does the deficit on the training days come from?
If you choose option 2 (an irregular diet), is the human digestive system able to handle the stress of this fluctuation? Or is the secret really to drop the quality of the food and eat, say, cakes or chocolate bars, and then a thousand extra calories become a small volume of food. In that case it seems a spreadsheet would be necessary—to avoid that the outlandish number of calories do not come with an equally spectacular amount of saturated fats. Few would complain of the opportunity to indulge in extra slices of cakes and chocolate bars. The trouble then is the accompanying (saturated) fat. Even if it's not the objective, one of the nice side effects of a workout is to develop a larger heart muscle and larger-flow arteries. It doesn't help if that happens while both become surrounded with fat deposits.
Update

Part of the problem is fear that my hunger triggers may be entirely off. They only signal a very slight extra hunger on riding days, which may mean a slow, inadvertent, and gradual muscle loss. The combination of potentially being hard to measure (slow) yet cumulative (gradual) muscle loss is what makes it worrisome.

Judging by the very existence of hitting the wall, it's not that hard to exhaust the carbs stored in the body. I understand that these carb stores increase with exercise, but meanwhile what mechanism does the body use to average out? Are fat stores really capable of building up and getting used in a short-scale cycle?
Either is fine - in fact on this timescale there's not much difference.
My suggestion:
I suspect that what's most satisfying for your body and your desire to measure will be somewhere between the two - probably something like 2300 Cal on your off days and 2900 on your riding days.  This should be quite achievable - a handful of cheese added to your pasta example and another energy bar on your riding days and you're well on the way.
Reasoning:
The human body is very good at averaging out calories burnt and calories taken in.  This is easily demonstrated: the recovery eating phase lasts several hours (though tapering fast especially regarding glycogen), and carb loading (not needed for up to 90 minute efforts) happens the day before the ride.  You'd see a weight fluctuation if you weighed yourself daily, but that happens anyway and hydration would affect that too.
If you're trying to maintain your weight and muscle mass, with that sort of level of riding, you should be fine with a sensible  balanced diet eaten to hunger - tracking your calorie intake isn't necessary, but if you want to do it, that's fine, except that your estimate of your requirements may not be perfect.
Your body can store enough glycogen for that much effort, so losing muscle mass to fuel your rides really isn't an issue, especially as you're snacking.  If you're worried, some small protein intake during/after the ride would do no harm (even just the little bit you get from energy bars with nuts in, for example).  I sometimes do a 75 minute early morning fasted ride (32km, just under 800  Cal which seems like a good estimate - yours seems high but not implausibly so).  In that case I start a protein drink towards the end, which seems to help my recovery in terms of muscle fatigue/aches.
I take your uneven pattern much further - every couple of weeks I do an all-day or even all-weekend ride, and then you really can't take in what you burn (Strava says 8000 Cal for Saturday's 400km).  The excess hunger lasts 1-3 days, but my weight recovers in a similar timescale (when I first started distance riding there was a permanent drop after each long ride, but as I didn't get weaker in the gym I don't think it came from muscles).  Yes there's some energy-dense junk food in there, but that's optional; I happen to like chocolate.
As for your worry about the stress of fluctuating intake - yes, it's fine.  Most of our human ancestors had no choice (could they afford much more than rice/potatoes/bread every day, with meat once a week - or what could they gather in season, how often did they hunt successfully) and anyway couldn't measure their calorie intake.  Your bowel movements might settle into a new pattern, but I wouldn't expect so much as a mild stomach ache