I'd like to take an extended break from the game, but...

[Dustytome]

One issue I see with an instanced system is that it might be quite a gil sink if people could buy a large amount of houses indefinitely which might affect the economy with all the gil being flushed down the toilet.

That's not an issue though as housing is an intended gil sink.

Have an option to "store" houses. All decor, furnishings and workshop progress will be saved and you will be given a ticket that can be redeemed on an equivalent empty plot (e.g. If you stored a large house, when you come back you can only redeem it on an empty large plot). When you redeem the ticket your house will be reloaded as it was when you left.

I think it would be better to just let the workshop/airship progress be kept regardless of the house, but nothing directly tied to house size. Any furniture you want to keep, you're in charge of storing or accept you'll have to go on a buying/crafting binge IF you manage to get a house when you return. In your example, a returning fc would have to find a large plot (of which there are only 216 per world at the moment) upon returning in order to redeem the ticket. Until they found a replacement large lot they would be stuck without anything they've unlocked.