The Dundee PSO has existed long before any EK flights to STN, so it was never intended to provide longhaul connections in the first place (remember that when the London route was operated on a purely commercial basis by Suckling/Scot Airways, it went into LCY). Obviously the primary purpose of the route is to provide a connection to the UK capital. If connections were of any real importance, the PSO tender would have specified a gateway better suited for that. So I really don't see a reason why not to move to SEN. For a short domestic flight, SEN would be a better travel experience anyway as time required at the airport for getting through the terminal, check-in and security and onwards to the gate area would be much shorter at departure and on arrival it would be a matter of five minutes from the aircraft to the train station.
As for "the PSO is not for the airline" - it is a tender and if Loganair feels fit to submit a bid for SEN that is cheaper than for STN, it would reduce the subsidy required. Unless there are compelling reasons why public money should be spent on a more expensive STN link, it would be a non-brainer to go for SEN. And I don't feel that allowing a few people a connection to a Ryanair flight for a tenner or to do a two-stop-connection on EK from Dundee instead of a one-stop connection from EDI, is such a compelling reason. Plus, unless there are other bidders (which apparently has not been the case for quite a few UK PSOs recently due to a lack of regional airlines). Loganair would be free anyway to only bid for a SEN route as the London gateway in those PSO tenders is never specified.