I think you misunderstand what it would do. Jumping would be just as fast but would necessarily require that Orkies be weaker since the player would have to devote two levels to Stabilize Phase Space which will make the Orky weak in some regard. Right now, one of the main reasons why it is OP is that you can send in a maxed out Orky which is incredibly hard to counter.
Something else I thought of was that you could probably give a jumping Orky a negative trade income since the precise amount is set in the upgrade file. I don't think negative income is taxed either, so late-game, it would be more a handicap.
Goa and I have also both made SM require both levels of Enhanced Phase Tunneling, further pushing it towards the late-game.
My assumption is that the "upgrade" the VR player will sacrfice will be the 3rd weapon upgrade (which increases damage by 20%)...
VR eco players will have no trouble getting SB mobilization and enhanced tunelling....VR in eco will have to get 4 civ labs anyway to actually play eco effectively (trade comes at tier 4), and really any vasari player worth a damn is going to try and get 5 civ labs for phase stabilizers...so, to get enhanced tunnelling requires only 2 more labs...
So, what does this actually accomplish?? VR SB's do 20% less damage than they could otherwise, the eco player has to get 2 extra labs and 2 extra techs (3 if you count the SB upgrade tech), and they need to spend some more money on the extra upgrades (really, only one more upgrade since you swapped out 3rd weapon upgrade....
All you've done is delay how long the VR eco is going to be able to overwhelm everyone with ridiculousness...definitely better than the current situation, but doesn't solve the issue by any means...
I like having two levels of phase stabilization, but something else needs to occur...Starbase mobilization needs to impose taxation (15% or 20%) or SBs need to cost 150 fleet supply or something because late game VR are still going to have jumping orkies, and still are going to queue up a 2nd and 3rd one right behind the 1st ....
Also, IIRC a periodic action applies itself first, then looks at the interval time...not sure if your buff system considered that or if I'm just being dumb and missing something...