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You can use Orca.exe to remove the CA.ProfilerInstalled action from the InstallUISequence and InstallExecuteSequence tables in the "main" MSI. Then you can install the Management Console side by side with the Application Profiler.
It's not officially supported (nor officially tested), though (as is probably obvious from the default "cannot be installed" error message .)
Thanks I'll give it ago, its a mild annoyance everytime I do upgrades, that this may help. They'll never technically be installed together, outside of the capture process.