These SE Transmissions are effectively identical to the manual gearboxes, only with a centrifugal clutch on the SE5's & an oil pressure based hydraulic clutch on the SE6's, and both have flappy paddle operator initiated but computer controlled electro-solenoid activated 'quick-shifters', and a computer triggered 'auto-downshift' as a 'protective action of last resort' in order to avoid operators trying to put too much torque thru too high a gear at low road speeds. :thumbup:
So maybe
some of what it sounds like you're surmising isn't
really all that likely, but early in the piece many '
new to hi-revving V-twin motors with centrifugal clutches' operators, especially those more used to hi-torque low-revving motors
did flog their SE5's by trying to keep & run with their revs waaaayyy too low &/or shifting up waaaayyy too soon!! :yikes:
The SE5 centrifugal clutches might
start to engage as soon as you apply throttle, to get you going and let you run at slow speeds, but they aren't really 'fully engaged' until something like 3500 rpm, so those operators trying to idle along at maybe 1,000 rpm in any gear, and especially in any gear higher than First, were/are really doing their clutches a disservice, & that in turn tends to be pretty hard on the oil that everything from the engine thru all of the transmission runs in!! :yikes:
So back in the day, there were quite a few pre-2013 Spyders across the board & those V-twin powered Spyders that continued up until 2016/17 that ended up with clutch issues, so many that in around mid 2013 there was that clutch upgrade that beefed up the internals to withstand that sort of abuse a bit better; but that particular problem wasn't really resolved until the new models came out with the 1330's & their very similar but now 6 speed gearboxes and their oil pressure operated hydraulic clutch that basically engages pretty close to fully as soon as the engine revs anything much higher than idle! And no, you can't readily swap in one of them on a V-twin, altho I guess if you want to throw enough money at it, anything is possible!

However, it does sound a lot like you might have scored one of those abused pre 2013/2016 V-twin clutches! :gaah:
Good luck with sorting it all out. But once done, just so long as you instruct any rider to remember to build the revs up over at least 3500 rpm before shifting up, and then ride to always keep the revs up above that, they shouldn't really have any issues &/or further clutch problems. There are quite a few of the V-twin SE5 Spyders out there now with well over 100,000 miles of riding like that with
absolutely NO gearbox or clutch issues. 
So they
can be a good clutch/transmission that will last very well, just so long as riders keep the appropriate oil & regular changes up to them, and they keep those revs up too!

hyea:
Again, Good Luck! :cheers: