The distlib ones are modified on install to include a script file at the end, which the executable knows how to find and launch. This includes the absolute path to the venv’s python.exe.
The venv’s own python.exe isn’t modified, but knows how to locate a nearby pyvenv.cfg and use that to launch the correct python.exe.
Process launch is unfortunately very expensive on Windows, and can be made drastically (5-10x) worse by certain antivirus software. We avoid the worst of these in Python by not modifying the executables, but because distlib does modify theirs it’s likely that they’ll trigger a deep virus scan each time they’re launched (the various exe packers usually have the same issue).
With a properly embedded Python, you can avoid all of these for your app (especially if you include enough native implementation for the critical part of the fastest path). But if you’re relying on users installing your app into their own runtime, there’s really no option but to launch a couple of executables.