Are 23mm tires on a 25mm rim (21 mm internal width) safe? Odd situation here, I'm putting together a 2nd road bike (I commute daily and need a backup for when my main ride needs adjustments, part replacements, etc).  To stay on the economical side, I purchased Zipp 30 Course aluminum rim-brake clinchers:

https://www.zipp.com/wheels/30-course-rim-brake-clincher/

rather than going with carbon.

These rims have an external width of 25mm and a very wide internal width of 21mm.

At the time I ordered these I was not aware of the internal width being the driving factor for how wide a tire ends up being after mounting/inflation.

I mounted 25mm Continental GP 4000 S II on these rims and after inflating the tires are 27.5mm - 28mm wide.

The clearance with the frame I'm using (which is stated to take up to 25mm wide tires) is extremely tight at the rear, where the tire passes both the seat stays and the chain stays.  I haven't finished assembling the bike yet, but the clearance is so tight I'm pretty certain there will be a clearance problem under load.  If anybody is curious the frame I'm using for this build is a Dengfu R02 http://www.dengfubikes.com/ROAD_FRAME/131.html

Can I use 23mm wide Continental GP 4000 S II on these rims?  If I try, will they mount?  And more importantly, if I can get "23mm wide" tires (which would probably end up being about 25mm on these rims) to mount, is this a safe configuration?

It would be a shame if I could never use rims I just paid $950 for, however I consider safety to be far, far more important.
Actually, tires narrower than rims have an aerodynamic advantage, there's a "105%" rule of thumb that states your rim should have width equal to 105% of measured tire width. That's why aero rims are getting wider year by year, all in order to accommodate a wider tire, which also brings comfort and lower rolling resistance. Here's an explanatory article (archive) by Joshua Poertner, who used to be a technical director at Zipp (source).

In your situation, the only factor that limits tire width is frame/fork clearance, you will be fine even with a 23mm real width tire, not mentioning a Conti tyre that runs wider than claimed.

On a side note, 25mm outer / 21mm inner rims aren't even that wide by today's standards, there are 28mm (I own a set) and even 30mm road rims available.

Update: recently, I had the same question about 26mm tire on 25 ID rim and some people pointed out this might cause riding on sidewalls during sharp turns. Something to keep in mind for sure.