Currently there is no built in functionality in CA Top Secret that will compare two security files. I am not aware of any 3rd party software that has the functionality you are looking for.
A user written program could be written to compare the output of the datasets created by a TSSCFILE TSS LIST(ACIDS) DATA(ALL).
A TSSCFILE TSS LIST(ACIDS) DATA(ALL) would dump out all the records on the security file into a dataset.
A user written program could be written to generate a report that compares 2 security files.