That boot is history.
If your transmission oil level is dropping so is at least one gearbox oil seal, and given where the leak is, my money is on the rear trans seal.
I have had driveshaft flange bolts loosen and let go (it is quite a mind focusing event when it happens let me tell you) and as a result I am firmly in the "buy new bolts" camp, they are no expensive against the cost of the seals. The boot is quite cheap too.
Best thing ever for fitting a new boot are some angled artery forceps - these are surprisingly cheap brand, can be had 2nd hand on fleabay and if you have a friend in the medical trade you might be able to hit them up for three of them. I was amazed at how easy they made the "fitting new boot" job.
As your gearbox is coming out, I would buy all new seals and a new clutch plate in addition to the boot and bolts. You may also need a new pressure plate/driven plate combo, but you won't know till you get there.
Oh, a few last things - you can get the drive shaft flange off by scrounging a suitable round piece of plate, at least .25" in thickness and drilling 6 holes in it - 4 to bolt it to the output flange and two tapped to suit your favourite bearing puller. Or you can buy a special tool for around $75US.
The output shaft is on a taper - this is a not too bad idea but it requires very careful putting back together - you can check if anything nasty has happened using Prussian blue, but if it was together properly when you took it apart, chances are this would tell you nothing useful.
Do coat the tapers in grease when you seperate them so that they do not ruse and do polish them furiously after a careful degrease before putting them back together (clean and DRY is the secret). This is one of the more "careful" jobs you do on our Boxer toys.