Question: I'm wondering if there is any research about if there are better, or at least "not so bad" times of a child's development for a father to less available. (Not completely absent, but time would be limited to weekends and a bit most/some evenings on weekdays.) 

Situation is a two-parent household with one 3 year old daughter. I have the option for a rather high-paying job, but it would require excessive (to me) commuting, like 2 hours each way. If it were temporary with the goal to move closer, it would be fine, but in this case it would be at least 6 months, likely a year.

Answer: 
Based on my experience as a military kid, my husband's experience as a military dad, and my experience as a foster parent, the biggest factor is how the limited schedule is presented to the kids. For smaller children, like your daughter, they tend to quickly adapt to the new normal, as long as the parents are satisfied with the way things are, and are available to the kids when they are present. If the parents tend to view the schedule as something negative that they need to apologize to the kids for, or make up for by going overboard in the time they are together, then the kids will cue off that. 

As a side note, the schedule you describe (weekends and a little on weeknights) is fairly common with small kids and working parents. My husband and I both work, and I get weekends and a few hours on weeknights between picking the kids up at daycare and bedtime. My husband gets even less, as he works later, and the kids are well attached to both of us.
Well, I can talk to you from my experience with my oldest child. I got pregnant at the university, and her father was 400 km away because he was at university too. Her first three year she only saw him like two times a month, two days each.
She is now almost 6 years old, and love him so much. But the relationship with me it's better, because we spend a lot of time alone, the two of us.
So, there's a bond between them...but sometimes it's hard for both to have a relationship.

IMHO, it's better to be absent when the kid it's very little, and doesn't miss anyone, except for the provider of primary necessities (AKA mom), but I don't have a source of that, only, like I said, my experience.