I decided to tinker around with the patch file to see if I could fix the time warp bug. I changed "$rescale-factor" to "$atmo-rescale-factor" on line 107 of the rescale.patch file and that seems to have done it. For clarity, the full line should look like this:
atmosphereDepth: $value * $atmo-rescale-factor if $value != null else null;
Then from the main menu in-game go to Settings > Mods > Patch Manager > Always Invalidate Cache
Restart the game at least once while this is set to Yes.