I bought one spray can of the minwax water based stuff ( Maybe you are using the brush stuff) and I could not get it to lay on a smooth coat.
Before you tell me I do not know how to spray, I have been using rattle cans, Syphon feed auto sprayers, air brushes and LPHV guns for years.

I have also done several playfields with spray can Varethane and have never had that happen. Definately a bummer.
As OP said, maybe it will ill dry out to the correct color.

I will absolutely agree that the minwax stuff is tough. I used what I had left on a gun stock for a rifle game restoration. Did not spray out glass smooth but it is as tough as nails.

It sounds much quicker than Varethane if you use the sprayer.

Thats excellent news.
I hope it comes back 100%