Nah why would the floorpan need to be attached to the sill with metal - just slap fibreglass or some silly putty on it :P

Yes its a pretty integral join in the grand scheme, so get it welded. Thankfully its a pretty easy area to cut out (to clean metal) and get a decent rectangular piece shaped up to drop in. Not a hard job really even for a DIY welder with some patience. Prep is key tho if you don't want to be doing it again in 12 months, theres clearly alot more rust sitting under the remaining paint and probably under that plastic sill trim, so either cut it all out, or take it right back to clean metal with a flap disc or wire brush and see if theres strength in whats left to weld to.