I agree with Wonshu, the best workaround is to simply create a software instrument track, insert Klopfgeist, create a MIDI region with the count-in notes, and move that region as desired when you start playback from a different position.
I listened to your two samples and there's definitely some processing other than gain change between the two.
If you can share the original project and give us the exact steps you took to reduce the level and get that second sample, we can try to reproduce?
I just tried setting 'Toggle Snap to Grid' to Command + F2 and it works as expected here.
If you set that command to any other shortcut, does it work as expected?
The cycle area does not affect how much of a track is frozen. The project end marker does, so moving the project end marker closer to the actual length of song does reduce the time it takes to freeze tracks.
I don't have personal experience with it, so I'm glad @Sascha Franck shared his. On paper it sounds like a great machine and I would definitely recommend it, yes!
These are take folders, you'd need to select the actual audio regions inside... maybe flatten the take folders, move them to their original recorded position, then pack the take folders again.
Make sure you save your file as a copy so you leave the original untouched and work in the copy, just in case.
Now in that copy, choose all audio regions and - assuming you didn't do any editing of your audio regions like moving or copying recordings around the Tracks area, choose Edit > Move > To Recorded Position.