The rope will be fine even if a bit mucky, sitting chain on it won't hurt the rope but does leave a nice saltwater laden bed
for the steel
chain to sit on, something worth thinking about. If the rope will get used very little sitting it up to one side isn't a bad idea.
A thimble won't go through the winch
and if you try there is a high chance it could cause damage to the winch
or the rope, possibly both, we see it more than we should.
2 options now - 1, put a thimble in and manually tweak it around the gypsy
each time. A bit of a pain but it would mean you have a nice long spare line should you require it. 2, splice it to the chain and it will go thru the winch well, assuming it's done right. Poor splices are real easy to do, the right splice is no harder.
The good rope to chain splice done right is perfectly fine and no weaker then a equal thimble splice, that's been well and truly proven.
On a Lofrans
running 10mm (3/8") chain 5/8" 8 braid (octiplait) works damn well and is a good match. Try to buy a T66 grade Nylon version, it will cost a little more but easy outlast lower grades. Think 'lifetime' cost rather than purchase price
it will save you money
over time. That's now also well proven.
As always, there are rope and chains and then there are ropes and chains, the above is talking good stuff and may change if you buy nasty stuff.