To be honest you are not the first to report this problem and I already tried to explain why meridian flip may not occur (regarding indi-eqmod at least, I don't know for other drivers which are using alignment).
Eventually there may be some misunderstandings between developers. Here is my understanding:
Meridian flip is used in order to keep down the counterweights of the mount, avoiding your equipment to hurt the pier. If your mount is perfectly aligned, the mount meridian coincides with the celestial meridian, and a meridian flip should occur when the mount crosses this unique meridian. Now suppose you turn the pier of your mount 45 degrees to the west. The mount is misaligned with deltaRA = 3.00 hours and the alignment system will correct that for you and track your target as desired. At that point, if the driver performs a flip when the target crosses the celestial meridian, this will result in a counterweight up position, as the target is still 3.00 hours before the mount meridian. And that's not what you want in order to preserve your equipment. That's why indi-eqmod may not perform a meridian flip if the corresponding goto is still before the mount meridian.
To sum up a meridian flip is related to the mount coordinate system and should occur at the mount meridian, never at the celestial meridian. And that may be before the celestial meridian when the pier is shifted to the east.