The ‘*_count’ bands are created by the mosaic step. They count how many source pixels contributed to one target pixel. This is often useful when mosaicking multiple products. They are also used in the valid expression of the B# bands.
You can remove the count bands but you also have to change the valid expression of the B# bands.
I agree that it would be a good option for the Mosaic to disable the generation of the count bands. I’ve put it into our issue tracker.
To ease the workflow a bit it is sufficient to create the spatial subset only on one of the products, e.g. the L5. When collocating the products afterwards and using this one as master the other will be tailored to this spatial extended.
You can also do the spectral subset at the same time as the spatial subset or the mosaic.
What I haven’t yet understood is the last error you report.
I think you can simply delete the collocation_flags