I was looking for information about MuTect2's accuracy and found a pitfalls summary on Read the Docs. Some of the examples are alarming. Will these issues be fixed in an upcoming version?
GATK4 Mutect2 will call somatic variants at the allele-level. Also, the filtering functionality is separate (in FilterMutectCalls) so that users may tweak parameters according to their research.
The Read the Docs summary appears to be for the GATK3 version of MuTect2, which was released as a BETA tool and hasn't been developed further in the last year. This is because all development efforts have been in GATK4's Mutect2. Please let us know if the new GATK4 Mutect2 does not address your concerns.