I wish I had the answer to this, but to be honest, I haven’t seen many players going between different playing modes on the fly.
I know that Steve Morse now does, I think that’s due to arthritis. So in recent footage of him you can see him switch between elbow motion and wrist motion. He doesn’t do it mid phrase, I don’t think so anyway… so that’s where the opportunity to alter his setup becomes possible.
I would say that there will always be a difference in how the economy stuff feels compared to alternate.
It may be a case of purposely practicing a phrase you are very comfortable with using economy and then playing another phrase you are very comfortable with using alternate picking. Trying to close the gap, between phrases.
I’m not sure if that’s any help at all… but I see no issues with either mode of playing, so I wouldn’t change how you do it in an attempt to make them feel the same.
Purposely practicing switching between the modes might be the way to go, if nothing else, it might reveal any specific reasons you are having difficulty.