As of the latest update, pressing "CONTINUE" in the Mors Longa menu properly keeps track of your distance, and therefore the enemy level.
Due to engine limitations, you'll eventually have to stop playing / loading into a map because performance will always go down. But now you can preserve your progress and reset performance by loading a new map with "CONTINUE," though you still can't keep your vehicle that way.

The best way to enjoy the mod IMO is to figure out about how many kilometers you can go before performance gets unpleasant, and plan on stopping at the merchant shop closest to that distance. Sell anything you can't fit in your inventory + chest, go to the menu, then hit CONTINUE. Just remember not to get too attached to any vehicle you find near the end of that distance.