I have a neighbor that partially sunk his. He has about 3 feet deck all the way around with access via a removeable lattice. He feels he should have put it in the corner because he has found that nobody uses 2 sides of it.
If you partially sink it make sure the access panel can be removed. This may include making a removeable hatch in the deck. If you have it fully sunk and its in the middle, have them wire an extra outlet under there. This is for a trouble light/power tools plus the spa techs will thank you if/when needed.
If you place the tub at the corner of the deck, try to make the access panel available behind the lattice of the deck. Also if you have planned on setting the tub in a specific way (has stairs or notched corner as an example). The access panel may be in the wrong position. You may have to ask them if the pumps/moter/etc can be moved to a different wall.
Then there is the cover, the cover lifters have to come off. More work, unless you design your deck like a convertible. If so send me the details! LOL
Another consideration would be, in a flush mount the chance of falling in (in my opinion) increase with the cover off. Also the step in could be a big one, if no steps or stairs are built into the tub. Whereas above/on the deck it would be like sitting on a chair and swinging your legs in. Also make sure your deck can support the added weight.
Hope this helps,
r100rs