Hi 
I have two guitar amps that have auxiliary inputs designed for audio players to play a track for practicing guitar to.
The aux inputs bypass any 6.5mm guitar input shaping, but the manual does say the left and right channels are internally summed.
Each unit being a mono amp, and most existing music player cables being 3.5mm stereo, this makes sense.
I want to transformer isolate the output of each channel of the music player, and feed left and right audio into separate amplifiers.
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I could just go ahead and connect left to the tip of one input plug, and right to the tip of the other.
My obsessiveness doesn't quite know where it sits with this. I'm aware it could just be a couple of resistors inside.
If I understand you correctly - you have a stereo source that you want to send to two amplifiers - one for left and one for right.
This is simply a case of well just that - you send the left to one amp, and the right to another. You can get Y cables for this - stereo plug to two mono plugs. One possible concern is groundloops - since your source has one "ground", the left and right share that ground, and so, both amps will have that connection. Many amps have the ground connection earthed, so their grounds are also connected via the mains plugs earth.
In this case, you would need 1:1 audio transformers on each of the amps inputs - or perhaps one just one, if your "source" is floating, as in battery powered.
Is there any situation with summing the signals internally, where it wouldn't be wise to connect a single channel to both the tip and sleeve (Left and Right terminals) of the input 3.5mm plug?
I would think it wouldn't be wise in any situation - the left and rigth channels may (and will) be prodicing different signals, they may share a common ground but that is all they have in common. The
only situation I can think of where it wouldn't hurt is when both left and right channels are providing the exact same signal, so tied them together would simply provide twice the possible drive current. However, I don't think that situation exists apart from having a mono source that is connected to other sources via a stereo plug ?
Think about it, if you have music that has a part where it is louder on the left channel, then that signal will be of a high amplitude. By connecting it to the the right channel (a lower amplitude) they wil fight eachother, and current will just flow from one to the other. I suppose it would just "average" between the two but that isn't necessarily a good thing.
Honestly I think you're over thinking it - but the part about ground loops is important