I’ve got the Film Carrier Mk1, and it keeps all film within very flat, whether at the first frame or the last. I wouldn’t worry about that aspect at all.
The issue with strips of negatives is the distance between the actual image area and the advance mechanism; there is about a two frame distance.
If you’re working with strips of 5 frames, you’ll have to manually insert the strip and advance the first two frames (by pushing the strip by hand) before it reaches the advance knob. Then the last three will go quick.
Negative Supply say that they don’t recommend it for strips of less than 4 frames, however I shoot every frame I can get on a roll and cut into strips of 6, so I usually end up with 3-4 frames and a little extra left. At first I took them at their word and my way to deal with it was to tape a length of leader into the small strip and feed it in that way. But after several rolls I realized there is enough space to push the film forward with your finger, so that’s what I do.
Negative Supply is right that the carrier is designed for uncut rolls - it’s the quickest way, and given how fast it goes my process now is to scan before sleeving the film.
Going through the back catalog will take some extra time though. Still better than any other way! (That I know of)