Same filename on different RTC Component folder

Do you mean within a single stream, or across all streams?

If you want to have it during check-in, it will crate lot of overhead to RTC which isn't ideal.

You could do some passive scripting do this. It's a lot of work though. This could be a like a scheduled script which can run every night.

Custom server level check-in preconditions/advisors can be created for RTC 6.0.5 and higher. This is described here:
  https://jazz.net/library/article/89651

Note that Karthik is right and the computational requirements/performance penalty will likely be huge dependent on the number of components and files per component.

Also note that the built in pre-conditon "Restrict Check-in of Resources With the Same Name" only looks at the same component on the same repository workspace and not in all the history of the component, likely for a similar reason.