I wouldn't think you'd need to pad the 1st met head in a pair of VFFs.
Don't forget, "Morton's Foot" is a perfectly functional foot. Entire civilizations had "Morton's Feet" (Greeks, Celts) and they were vibrant powerful cultures. They weren't hobbling around on crippled feet.
What they had were shoes made for THEIR kind of foot. (or sandals/soft shoes) Morton's foot only becomes an issue when you try to cram a long 2nd metatarsal foot into a shoe designed by and for folks with long 1st metatarsal feet.
(and, of course, they weren't constantly exposed to flat hard surfaces, which I still swear are the bane of ALL modern tootsies)
Morton's foot isn't just a longer 2nd metatarsal, it's also a differently shaped cuboid bone so the foot really does move a little differently. It's also a longer foot, so it's easy to develop hammer-toe because of shoes that are too short in the toe box.
VFF are enough like barefoot that I'd think they'd let your foot do its natural thing, unhampered by shoes designed for a different kind of foot. I'd just suggest you start your VFF running on dirt trails or grassy fields so your foot muscles have a chance to wake up and gain the strength to support your mets properly before you start running on hard flat surfaces.
Knot-doesn't-have-Morton's-foot (but does have dropped 2nd met head)
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson