The size of your tandem is indeed an issue.
Tandems, recumbent bicycles, tricycles, cargo bicycles and other bicycles over 2 metres in length can only be transported on SBB trains of the categories RE, S and R.
It will be a problem for the IR train to Göschenen as this train does not have sufficient space for such long vehicles. It is operated by SOB.
A tandem of this size would require two bicycle day passes.
Kindly check (and ask for a written confirmation) with the railway operators whether you are allowed to take your tandem on board.
For IR 46:
For the train Göschenen to Andermatt:
https://www.matterhorngotthardbahn.ch/en/stories/service (see website footer)
It would be a lot easier if you had two regular bicycles.