Actually, the Manfrotto 099b has a 5/8" threaded stud only at the top like your stand, but the bottom has a socket which will fit over your stand's stud; no Rapid Adapter required. However, since you have that adapter stuck to the top of your stand that could be an issue. Just tested it on my 099b with a similar 3/8 to 5/8" adapter; while the threads of the adapter fit into the socket of the extension, that rim along the base of it will not fit and you won't be able to seat it properly or at all. I think you'll have the same issue trying to fit a Rapid Adapter over it.
One way or another I believe you will have to get that adapter off your stand's top stud if you want to use an extension. Maybe use a pair of vice-grip wrenches after another shot of WD-40: one to grip the frozen adapter, one to grip the stud. It's also a good idea to use a
Rapid Adapter instead of threading your stereo bar directly to the top of the stand to minimize an issue like this (ie: stuck/frozen threaded adapter).
BTW, the 099b is a great piece of hardware and I use mine quite a bit. As far as the stability of zip-tying 13 feet of stand to a seat... personally, I would use
a lot of zip ties.
