Well, that took some doing. But it now works with one ship in play, multiple ships could be a problem but I'll cross that bridge later...
As suspected, any input manual control bar doesn't just stop the 'tick' part of the command, but the entire command and any attached 'includes' as well. In order to get around that, I've got to make the new command record some variables at 'U' level, which a rule from another machine can then read and check against. If the rule in the second machine can't find either the expected value or the exit value, it re-issues the command.
In trials, my ship now approaches the intended target untill an enemy tries to get too close. In which case it'll try to fly around the enemy, and if fired upon will then engage said enemy. Finally, with the enemy neutralised, our ship proceeds to it's initial destination.
Still a few things to sort out, but it's promising...