Don't quote me on this but I think it would be possible.
Take the Scorpion full exhaust and header system you can buy for example.
You can buy just the scorpion end can and connect that to your stock pipes=scorpion end can connects to the same place as stock=scorpion head pipes will also reach same location as stock pipes=you could use scorpion pipes with original end can.
This conclusion is based of course on the assumption that the stock end can angle can be adjusted slightly if necessary depending on how it is mounted vs how a aftermarket end can is mounted. But from looking at pictures, all aftermarket companies have made their full pipes systems so they end at the same location as the original ones.
As for the remap, I've got no idea, sorry. There are a few threads on here about necessity of remaps after changing full system vs just end can
The question is, why would you swap the pipes but not the end can???