My theory is that, at the time that rule was written in the RRG, it simply did not occur to the designers that your squadron might be engaged and still able to attack another squadron that it's not engaged with. This can arise due to obstruction, or special abilities such as Snipe.
(i). The rule could have been simply worded as "if you are engaged, you cannot attack a ship", except because "cannot" is absolute and not subject to exceptions (I know, I know: only when it appears on a card... but arguments would have happened anyway). Or perhaps "if you are engaged, you can only attack squadrons".
(ii). Alternatively, when FFG were confronted with the situation addressed in the FAQ, they could've chosen to rule it thusly: "if you are engaged, you must attack a squadron you are engaged with" (i.e. without the "rather than a ship" qualifier limiting its context). But they did not, and instead explicitly stated that (i) was the intended reading of the rule.