The agreement in the case of “tu étais réveillé(e)” for example depends on the sex of the person who is talking/whose you are talking to (the subject). There is no indirect object here. It is a simple agreement like “tu es intelligente” when you are saying that to a girl.

The agreement in “elles s’étaient écrites pendant des années” (and so “tu t’étais demandé s’il était allergique” is different, because you can say “à qui / à quoi / de qui / …” after the object that means it is an indirect object. And in that case indeed the past participle never agrees, even with “être”. As you may know, past participle agrees when “être” but not “avoir” in the case of a direct object.

You are right, there shouldn’t be an agreement.

As you can see, both t' and s' are indirect objects here : to whom did you ask etc.? to whom did they write ? etc.

As per the rule you quoted near the end of your post, when reciprocal verbs take an indirect object, the past participle does not agree.

Therefore it should be:

Tu t’étais demandé s’il était allergique.

Elles s’étaient écrit pendant des années.