Right, i see what you are saying, it's based on the subgroup expression and how the hierarchy is drawn. I'll register FR, but no eta can be provided at this time.

The hierarchy is completely based on the subgroup expression at the top level, which can contain multiple items comma separated. The last subgroup will display aligned when there is a result as it's the final point of evaluation of the expression.
Create session subgroups - ConnectWise

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Thanks for your report.  I have discussed this with our architecture and information security teams and we agree we should find a way to make the toolbox behavior more predictable and clear especially when it comes to the required permissions. We do require the RunCommandOutsideSession permission to be able to run a tool from the host page, but not from the host client. we also have documented that the shared toolbox requires the TransferFilesinSession permission, and will make sure that we update this for the personal toolbox as well.

note: edited for a typo and clarity

This is something we are currently working on and hope to release in Q4. f you are interested in being a beta tester please shoot an email to ctrlpm@connectwise.com.

(anyone interested can do the same :) )