You simply misunderstand how AE's time handling works. The program does not "fit" a clip between a start and end point, it uses sub-sampling based on exact time. Hence you may see quantization artifacts when it calculates the discrete frames, especially with odd framrates like 29.97fps. Perfectly as it should work. You may simply need to adjust your time- stretch values by a fraction to better accommodate the underlying math rules.
99fps is the maximum AE frame rate so you can't have a 100 fps comp.
If you want your 100 fps footage to play back in real time at 100 fps then you'll need to use some other software. If you want your 100fps original footage to play back in slow motion then interpret the footage at a different frame rate and drop it in a standard frame rate composition. For example, if this were film and a projector, your would shoot at 100 fps and project at 24. This gives you every frame and slows down the action. That's the way we did all slow motion footage before you could blend digitally blend frames. If your comp is 29.97 fps then interpret your footage at 29.97 fps and you'll have every frame visible and a 10 seconds of real time will take 33.3667 seconds to play back. (10 seconds @ 100 fps = 1000 frames, 1000 / 29.97 fps = 33.3667 seconds)
If your interpretation is an even multiple of the frame rate you will eliminate the artifacts caused by blended frames. If you have time requirements that must be met then you will have to do some kind of digital frame blending. There are a bunch of options, but because I do not understand exactly what you are trying to do and you are working on an incorrect assumption about how slow motion works I can't give you specifics. "Stretch them both by 5000" does not make any sense to me. If you want 10 seconds of real time to stretch to 50 seconds then simply divide the frame rate by 5 in footage interpretation and drop it into a standard frame rate composition. You'll get some frame artifacts because 20fps is not evenly divided by any standard frame rate.
Frankly, I'm surprised you were able to make a 100 fps comp; I thought the upper frame rate limit was 99 fps.
And here's a question: once you render out a 99 (or 100) fps file, what are you going to use to PLAY IT BACK AT THE PROPER FRAME RATE? That ought to be a good trick.....