Okay, I think I have some more information that might be helpful. Please read paragraph 5.20a of the VP-X Pro installation manual, page 38.
The VP-X folks do not support the limit switches and they recommend that if you use limit switches, that you operate outside of the VP-X. Use the VP-X only to power the flaps. However, they go on to say that the limit switches can be used with some "risk and trade-offs". I believe the concern is that the VP-X sets the full up and full down positions using the internal potentiometer and not the limit switches. So I suppose you could set these limits just prior to the end of the stroke in each direction. They caution that due to inconsistencies of the pot, however, it's possible that the limit switch could be reached before the set pot position. I would look at it as the internal limit switches are acting as a backup to the VP-X full up and full down set points. The internal limit switches will automatically stop the flaps when the full stoke is reached up or down. Their concern is that the flap motor might run on, which would be the case with external limit switches, but our limit switches are internal and can't be deactivated or bypassed. I don't see the problem, frankly, but I'll discuss with Chad and report back.