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The Mark VII's upgrading only happens in standby, so there's little difference--its not going to upgrade itself on the fly during battle. Also, we don't know if the Mark VII armor's nanotech upgrading requires it to be worn or not when in standby. The one depiction of it had Spartan-010 removing it repeatedly and it's not clear if she did so out of personal preference or to instigate the upgrading.
Regardless, if she's able to do that it should be simple enough to install the different parts of the MJOLNIR GEN2. I think its unlikely that everyone is like John-117 and wears their armor 24/7, but even then there's time for them to put on and take off their armor in preparation for combat situations.
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