Just had a complete clearout of my car, including (for the first time in ages - probably a good year and a half) the boot liner, boot floor, and spare wheel out. Found a good 30-40mm of water in the spare wheel well
Some rust forming as well, though at this point it all looks like surface rust with no deep penetration.
Spare wheel well by
CmdrFire, on Flickr
I've mopped it all out, and have left it all open for now to allow it to dry out whatever's left. Next week I'll go over it with a wire brush and see how deep it penetrates; if it's not too deep and it's only slight pitting then I'll POR-15 it all and won't have to worry about it again.
Not sure if this is common on Mk5s (people probably don't check that area too often) or if it's because of the OEM plastic boot liner I've been using since I got the car but some others with older cars may want to have a look (and I'm going to stop using that boot liner - the actual boot floor was damp to the touch when I removed it, so it could be the boot liner was the cause).