It's not possible to be compliant to both specifications at the same time as they have completely different use-cases. Also, I wouldn't concern myself with measuring the in-rush current of various devices...the USB2 spec is clear in that Hosts must provide a minimum of 120uF on VBUS. If you are interested in learning why, check out section 7.2.4.1 of the USB specification...it's more about preventing VBUS droop than it is about protecting devices from excessive in-rush current.
All that said, it is possible to do what you are suggesting...but there exists the problem that you need to know which mode you wish to connect in BEFORE you actually connect. In other words, the appropriate capacitance needs to be present upon device insertion. This may not be an issue depending on your particular implementation, but it's something you need to be aware of. Take a look at the AM335x GP EVM for an example of how the capacitance is switched between Host and Device modes...it's not ideal by any means but it is functional and serves the needs of an evaluation board.
It's also important that you are using the correct connector for your proposed implementation (GPIO-switched capacitance)...the only valid choice is the micro-AB connector.