Sounds like you’ve previously had penicillin and not reported the side effect, so that the GP could assess at the time if it was the antibiotics that caused the thrush, which means it’s not listed in your intolerances.
It could have just been a coincidence that you got thrush last time, and it wasn’t assessed as being due to the antibiotics, so the GP sounds like they advise its more important that you take the best antibiotics to treat your foot infection than leave your foot untreated because of the risk of potential thrush which is easily treatable.
If you take the antibiotics and get the same side effect then you should ring and discuss it again, then the GP can assess whether it happening multiple times means it is an intolerance and can list it on your records. They can list intolerances, I have statins listed as a mild intolerance for muscle aches.