Thanks for the response, guys. I have indeed created my own workaround by now.
If anyone wants to add abilities to certain commanders that do not have any upgrades assigned to commander_abilities, simply use one of the original abilities, change it to an always_on activation, hide it from UI, and have it add a custom upgrade. This upgrade can now serve as a trigger to a copy of the original ability or whatever new ability you want to add.
Hope that was not too confusing.
I know this is a very late reply but yes, the Brits are very tricky to mod and it does seem that their commander abilities are added through an invisible/locked section of the AE.
I used to do something similar to your method for my doctrinal Tulip rockets, which was to have it as an ability that you had to then click in order for it to activate. This worked but was slightly annoying as it's not an ideal method (you're not supposed to have to click passive upgrades to activate them) and the AI couldn't use them.
However, there is another workaround for the Brits - at least for certain commanders. Several Brit abilities do in fact have a passive upgrade, such as Flamethrowers (needed for the squad upgrade to appear), Vehicle Crew Repairs, Hold the Line and Advanced Cover Combat. There are no doubt several others I have forgotten.
Using these passive upgrades it is possible to make a reasonable number of changes to the Brits' commander abilities, and especially in terms of using two upgrades (one true, one false) as requirements, and so using this method I've been able to achieve all of the Brit commander changes I wanted. It's tedious and means they're the most annoying faction to mod commander abilities for, but in general you should be able to make numerous changes this way. It's perfectly legitimate and means you don't have to piss around with creating lockout upgrades or any other imperfect workarounds.