OK, have come up for a temporary fix.
I made a dummy AF2 named "AF2_KFL1", and I renamed the AP_KFLL from the latest update to "AF2_KFLL_MCB". Here is what they do:
The "AF2_KFL1" file only contains the cement area that underlies the ground textures. It keeps the default ground from showing and also blocks the "AF2_KFLL_MCB" textures from showing (HS nodes, runway markings).
The "AF2_KFLL_MCB" file contains the airport facility features. It is the default AP_KFLL file from the V1.1 update but with the following changes to it:
- No cement ramp (not needed, it is in the AF2_KFL1 file)
- No more 1 meter taxiways (fixes the AI bunch up)
- Deleted X-Wind runways (Not needed at this airport)
- Deleted some taxiways that AI will never take for simplification
- Reposition start locations to be over the runway threshold
The files, along with a screenshots, are attached below. The only side effect of this workarround that I know of is that the displaced threshold arrows and threshold bars are missing, but I think this is an acceptable compromise for me.

As always, please make sure to back-up the original AP_KFLL file and place it somewhere safe. Then, place both these files included in the ZIP into the Scenery folder for KFLL. That is all.