I've read some comments on other yak forums about the TD scupper installs, but don't remember any long term side effects from mounting the TD in the scupper holes. I have also read where people use the scupper holes to secure their yaks to their truck or trailer with a safety cable run thru the holes. Yeah, the yak is tied down, but the cable is not and will/should bounce around in the scupper hole while in transit. I've not read of anyone having damage but doesn't mean they haven't had damage either. One advantage to the scuppe hole install would be the water temp would work better, but the hull could become an obstruction in terms of signal return, depending on the install. I would assume you could fine tune the placement to some extent or try another scupper hole to get better performance. Be the guinea pig for us LOL.
GO BIG ORANGE !
I meant to behave, but there were just way too many other options available at the time.