Hi
we have had a few floor issues inside and outside of warranty. inside the warranty we usually send it back to the factory if it's a serious issue (like your stain) sometimes we get a local vinyl man in and he works some sort of magic, but i can still see a repair join if i look closely. A couple we have fixed our-self, by joining under the edge of cupboards, by jacking them up slightly cutting underneath and joining there, VERY VERY time consuming as we need to make a template in paper first and usually only get one shot at getting it right so a lot of checking before we cut a sheet.
Out of warranty we let the owner decide, and i think the most popular option is rip it all out and lay self adhesive floor sheets that look like several planks, if you know what i mean. only trouble with that is if you open a bottom cupboard you see different pattern inside on the floor. but that is cheapest fix and pretty easy to do as i'm not a floor layer
so my advice .... (for what it's worth) take it back to the dealer and ask/demand for it to be fixed or replaced ...... (boss will kill me if he reads this) ask for it to be fixed at factory, it is their mistake, so the dealer may have to wear the cost of the stuffup, not a defect in the van which usually means jayco HQ pays, but they will probably join it under the furniture, you will never tell afterwards if they do a good job unless you lift a cabinet. going from past experience with ppl not happy with something on a van jayco has even replaced the van (one of my nightmare why won't this damm thing stop leaking!! jobs) so stand your ground and get what you want, jayco will come to the party.
as the vinyl is the third thing to go on the van (chassis, timber floor then vinyl) EVERYTHING sits on it including side walls, it's a important item to get right at construction. and also a easy item to damage afterwards. I used to wear black sole shoes at work but now wear tennis shoes as they don't leave marks like the black ones while your kneeling down, and every heavy item (fridge, cooker etc) goes onto scrap carpet if it needs to be set on the floor during removal, i even use a tray to put rubbish in as a stray wire offcut can cause a indentation if you step on it.
I remember they used to only glue the sheet down around the edge, but now they add more for some untold reason that must be a need to know issue, so it's even harder to fix the vinyl now.