It seems to just be a minor flaw/oversight in the design of the machine. That’s how everyone’s is.
I don’t think it’s that the hot signal is making 3/4 go haywire, the inputs just have multiple applications for different scenarios. My understanding is that If you want to plug in something with RCA cables that isn’t a turntable (like a tape deck, or your phone with a 3.5mm to RCA) you can plug it into phono1, select line 3/4 while sampling and the signal will bypass the RIAA phono preamp.
I don’t blame you for using your external phono preamp, Id experiment with the same thing if I had a nice one, but have you tried just going direct into the s2400 yet? The internal preamps on this thing are very nice quality!