I had some buggious experiences as well, in HSFX 5.0 & HSFX 5.0.1 Hotfix, using along with SAS Modact for HSFX.
6DOF, Catapoult & CTO MOD doesn't work in any setting as it should in MODS folder, JSGME or HSFX activated game.
Catapults reads to be already on by default, so I added lines to .mis files and conf.ini regarding the HSFX ReadMe.
With Carrrier T/O enabled all it does, it gives me new folded Wing at spawn and plane alignment. Catapult doesn't work by default, per added line or with CTO Mod "on". Tried using an older Mod for CTO, this gives me Malone's old Carrier/Catapult Freeze-CTD error, as far as planes begin unfolding wings, an explosion strikes, as the wings of all planes crash and with it my rig.
Works only when I'm spawning alone, can't push Autopilot, gets me same CTD, but Catapult worked.???
It wouldn't surprise me if I can't get to use these Mods in UP 3 too.
With HSFX I encountered Problems using the Recon Emils, I had no other Bf 109 Mod activated, so it changed somehow POV of my Stock E-7s, the whole cockpit mesh was moved and stretched. Deleting the Recon Emils solved the Prob.
Besides these old/new Probs it works flawlessly, really enjoying it despite some limitations.