Just noticed this post, and I have to make mention of a game I've been messing with for a few years now that might be of interest maybe, though I'm the wrong person to say how exactly it handles timing, but I believe it is an RDTSC game. 1998's Gunmetal from Mad Genius Software. The game's implementation of timing, however it was done, is rather broken.
In modern Windows, running the Windows version of the game, things run too fast. It was also an MS-DOS game (one of the last commercial titles for the operating system), but it runs rather slow in most options for modern play of DOS stuff, and I have heard that in scenarios where someone gets it running "bare metal" (FreeDOS or whatever on a modern CPU), the timing issues exist there as well.
Honestly I've been hoping to find someone with knowledge of timing stuff who might be interested in helping to solve this. I know there's been similar projects that have hooked into a game process to solve such stuff. Anyhow I also hope this can be a helpful example for what you're looking for. The demo is easy to find online, and preferably you should look at "demo 1.3" as the 0.99 demo is kind of borked.
EDIT: I should mention that I'm not the first person on VOGONS to have brought this issue up, and in the past the best things figured out was a hex edit and that, for some reason, VM acceleration stuff like KVM, WHPX, etc. can correct the problem. But these are either half fixes or require more effort than most would want to put in. Like, to clarify for the hex edit idea, it appears to differ from system to system what the ideal edit even is. This ends up being not all that different from the "time stretch fix" using dxwnd provided by the one fan bundle of the game floating around online, which I'm partially responsible for the existence of.
