Typical 3 hour road ride can see 16,000 revolutions of 1 pedal.
Imagine picking up a bag off the floor, 16,000 times. But you are twisted each time. It would get sore real quick.
Bad bike setups can quickly cause physical damage which can take considerable time to recover from even with good rehab.
I’ve experimented with heel wedging and took it one insert too far to examine the impact. During the etap London, after 100 km stopped in considerable pain, removed 1 wedge from each heel and pain disappeared within a few KM. It’s that subtle.
For the op, get fitted properly to your bike by someone who knows what they are doing. It makes a huge difference. Make sure they really understand feet and the critical foot/pedal interface, before you get anywhere near the saddle!