...So, I suspect cycling may be putting more sideways load on your joints than your physio thought it would, and trying the orthotics would be a good idea.
I think physios who don't have much experience of cyclists just equate cycling with 'low impact' without understanding that, while there is no 'impact' as such, each turn of the pedal causes a load on the foot which needs to be stabilsed at the foot/ankle joint. You can see what happens by standing on one leg in front of a full length mirror (hold the back of a chair for support if your balance isn't the best). Now lift your heel slightly (to simulate the pedal under your forefoot) and do a slow one leg squat - to about the same bend as on the bike. Notice the alignment (or not) of the toes, ankle, and knee and note how much effort it requires to keep your ankle stable in order to keep your knee over the second toe rather than drifting inwards or outwards. This is basically what you're doing each pedal stroke and the harder you press the pedals, the more likelihood of discomfort and injury (hence the exhortations to spin not grind the gears).
If you use an orthotic for running/walking, I'd suggest that in most cases, you'll need it for cycling unles you pedal with the pedal under the mid-foot (which pretty much removes the ankle joint from the equation and has a lot of supporters in the world of triathlon as it preserves the calf muscle for running). I didn't use orthotics for running (mainly because I was an off-road runner and fore-footer) but I do have very solid insoles for my cycling shoes which support the arch/instep to the point where they feel quite odd if I stand in them. This has the effect of keeping the alignment of the knee even when pressing hard - something I need particularly for recumbent riding
