I'm wondering if my lack of steaming habits had any effect on maintaining the clean mushroom.

Are you more likely to accumulate scale if you use the steaming function? I would guess you would be, but not sure if this part of the E61 would get hot enough to vaporize water.
I activated the steam switch once to see how the PID would react, but otherwise I don't do milk.

The mineral content in a dedicated steam boiler can increase as pure water is boiled away and the minerals are left behind. But your Alexia's boiler does double-duty as a brew boiler/steam boiler, so I don't see how occasional steaming could influence the boiler's overall mineral content.

This is a HX machine, no? Stream and hot water comes from the boiler. Brew water (all water that goes through the group) is from the heat exchanger. These sources are separated and only have in common that they are both supplied cold water from the same source (reservoir or plumb).

No, just a single boiler

I did a search and should have read further. Ughhh... The price threw me off as well.. in any case:

Would minimal (or no) steam use affect the brew function in some way? Being that the group draws water from the single boiler, and the fact that you found no scale on the mushroom, I would say that whatever is going on in terms of scale is not the cause of your situation. If it was, the scale would be quite noticeable on the 'shroom.

You can test the water using the Aquarium Pharmaceuticals KH/GH test kit. Check Amazon as it is quite affordable and gives a LOT of tests per kit. The basic knowledge is that you need levels of both GH and KH to create scale.