No.
Even with the MBAM Pro option on both my systems I haven't excluded each others files.
The only exclusion I have set in MBAM Pro is to excludes the c:\windows\temp\_avast_ sub-folder, which is where avast unpacks/scans files, so you don't want duplication of files in that folder or possible conflict. This isn't an issue in the MBAM free version as it isn't a resident application.