Yep, in my view the seam is just a rust trap so dispensed with it and any condensation (which this area can suffer from) runs down, into inner sill (which i thoroughly waterproofed) and out through drainage holes under the vehicle rather than puddling on the floor. The new sill is sufficiently rigid to not require a replacement floor section although you could weld one in if you wanted to. Personally I think a good movement of air is more preferable particularly if this area is normally covered by cupboards/fridge etc.
Chickenkoop and I tackled it in perhaps an unorthodox way but it seems to have put an end to any rot in this area and hopefully any subsequent problems. Not a bad job to do but in my view better to really go for it and do it properly rather than simply patch things up. In our view, there was little point in going to all the trouble of effecting repairs if we didn't address the root cause - which we've now eliminated.
Heres how it looks without that seam and using a complete panel. The section can now breath and any moisure has a pathway out rather than being locked in. Personally I think it looks right now and carries the natural line:
I should add, yours is quite extensive in terms of spreading rust and if you look at what we cut out during the job, you'll see why. It gives you the access needed to get in there and do the job properly. Don't be afraid of it - get in there and beat it.
