TL;DR: Don’t worry about it.
I’ve stayed in lots of temples and shrines in Japan, and their accommodations are effectively identical to “secular” Japanese inns: for example, you’ll be offered alcohol with meals, and boisterous drinking parties for traveling groups are not uncommon, particularly in Shinto shrine lodges. Of course, the usual rules of Japanese indoor etiquette apply, so take off your shoes before walking on tatami etc.
Only a few points may remind you that you are, in fact, in a temple:
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