I have a transporter but don’t use it with Roon. There is one place I see in the Transporter where I tell it to output S/PDIF rather than AES. Perhaps once that is set in LMS it stays the same. Start LMS, go to LMS > Settings > Player. Choose the Transporter as player and for “Digital Output Encoding” choose S/PDIF from the dropdown menu. Perhaps once set, it will retain that setting when you later connect it to Roon.
With the Transporter, I also have controls regarding S/PDIF regards turning on INPUT to the Transporter. That is, I have a rasberry rPi with S/PDIF output, and I can connect that to the S/PDIF input on the transporter in order to use the Transporter DAC (and in this case I have to select S/PDIF as the digital input for the Transporter). But again, this is all about digital INPUTS (AES, S/PDIF BNC, S/PDIF RCA, Toslink).