chimney flashing

[Roy Guard]

screw fasteners were installed on top of the step/counter flashing (you will have to zoom in). Is this acceptable in installation requirements, I can't find any place where it is acceptable but roofer is whining to replace, he wants to just seal the fastener.

Also, step flashing wasn't used along one sidewall of the chimney, is this really a problem (rather then using step flashing)