MIDI outputs are not suppressed when rendering but MIDI inputs are - on purpose - was reported as a malfunction a few releases ago and in general makes sense. In this case not.
Timing of such custom midi loopback device routings always is a little bit off. I think the better “fix” would be allowing to add the ability to create such layers in Renoise itself - somehow.
Could you guys consider then to add 4 or more routing ports that all simply send the same data? So even the same channel as the Input? Because that would open great possibilities of midi splitting.