It's a sneaky solution but it works for me.
I do a DoCmd.DatabaseTransfer acImport of the Autoexec macro.
Then I replace the autoexec with a blank one, using DoCmd.DatabaseTransfer acExport
The trick is that an Export will overwrite
DoCmd.TransferDatabase acImport,
"Microsoft Access", sSourcePath,
acMacro, "autoexec", "autoexecSource"
DoCmd.TransferDatabase acExport,
"Microsoft Access", sSourcePath,
acMacro, "autoexecblank", "autoexec"
I do that again for the second MDB
DoCmd.TransferDatabase acImport,
"Microsoft Access", sDestPath,
acMacro, "autoexec", "autoexecDest"
DoCmd.TransferDatabase acExport,
"Microsoft Access", sDestPath,
acMacro, "autoexecblank", "autoexec"
Then I can do all the comparisons for finding Diffs between the two MDBs without triggering the autoexec macros since I imported them and replaced them
Then I compare the two Macros I imported and then export them back to the databases.
DoCmd.TransferDatabase acExport,
"Microsoft Access", sSourcePath,
acMacro, "autoexecSource", "autoexec"
DoCmd.TransferDatabase acExport,
"Microsoft Access", sDestPath,
acMacro, "autoexecDest", "autoexec"
Obviously this solution only works using VBA in Access, but it does work.
Hope this helps someone.