I’ve put in a check for this in 11.7.0. Notenik should now automatically rename a Note titled “Template” to “Template 1.” Thanks for reporting this, and let me know if any further issues!
BTW, I appreciate your acknowledgment of the trade-offs here. It is a little messy having all the settings and the data stored in text files in a single folder. But there is a degree of simplicity and transparency, as you say, that comes along with this approach, and hopefully those factors outweigh a bit of messiness, at least for some of us.