I have both sets of inputs on my Focurite 18i20; Line L+R from main and spdif git/Master Left. Asio at 16 samples 44.1Khz 24bit.
Indeed, I can confirm this behaviour with the latest firmware 5.4.1
Main line inputs arrive first, then, spdif.
spdif "git" which is on the left spdif channel arrives about 1/2 faster than the difference between line and spdif "Master Left".
This is with a profile with 3 effects in the first 4 blocks before amp.
However, if I then turn the 3 effects off, then, the behaviour is the same except the spdif "git" arrives about 7 times later than spdif "Master Left vs Main outputs.
Weird behaviour. I tested this last year and in 2016 and I'm sure spdif was faster than using analogue cables.