[Android General] Oswald Boelcke:
First my configuration: RR v5.8.5, custom Boeffla kernel with Boeffla Config App, Magisk v14, Magisk Manager v5.3.5, Official Xposed Framework (sdk 25, arm) v88.1 by rovo89, Xposed Installer v3.1.2 by rovo89, XPrivacy and a few other things.

Please be aware that the official Xposed framework only works with rovo89's Xposed Installer; with the modified Xposed installer linked in the unofficial Xposed framework thread it won't work.

For many months now, I'm only using Nanomod and nothing else anymore (besides the backends I additionally wanted to have). Please let me reiterate that I only use Nanomod as Magisk module, and actually I don't have experiences if it gets installed to /system. Why should I change a perfectly running horse? And to answer your questions first:

I always flash Nanomod (in my case only microG, patcher and if required setup) through my TWRP v3.0.2-1. I once tried to install via Magisk Manager but had problems and since then I refrained from it. Doing it through TWRP isn't slower and additionally offers me a chance to wipe dalvik and cache. Just as a remark: Update of Xposed through the Xposed installer works perfectly but always choose the option "...through recovery".

No requirement for the module FakeGapps if Nanomod patcher is used.

If Nanomod is used, no need to modify anything in Google Play Store (except the settings to your desire). No need for bla.bat etc.

If you use Nanomod and deside to install Nanomod's modified Google Play Store version, no need to additionally install FakeStore. However, please be aware that later on F-Droid indicates you that a BlankStore with exactly the Play Store version number is installed; just don't care.

My general advice for a clean installation would be (I hope I don't miss anything):

Boot into TWRP and take your Nandroid backup.

Wipe dalvik/ART cache, cache, system and data.

Flash the ROM of your desire. If your ROM inherently supports microG/signature spoofing you can forget the later step with Nanomod patcher.

If required flash a custom kernel suitable to your device and ROM.

Flash Magisk (currently v14; it's stable but if you want you can try the betas). Magisk is automatically going to install Magisk Manager (currently v5.3.5).

If you're using a Samsung i9305 I suggest to flash now the official Xposed framework (currently v88.1, arm, sdk25) by rovo89. However, it's you're decision to flash any other framework that hopefully works for you.

Flash the Nanomod-setup-zip. The Aroma installer let's you select whatever you want. I personally always only go for mircoG with Maps v1 (still required for some apps) and Google Play Store but it's you decision and desire again. Select a location for the .nanomod-setup file. I recommend either internal storage or external SD as it's wipe-safe there.

Flash the Nanomod module of your desire. I always only use Nanomod-microG as I've no need for an elevated F-Droid or any other applications to be installed by Nanomod (actually, I'd issues especially with battery duration when I used the full module the first and only time - details are available somewhere in this thread).

Flash the Nanomod-patcher.

Reboot into system.

All following steps are now to your desire e.g. when to establish WiFi or mobile data connection. Somewhere in the thread I described my personal best practice in regard to privacy.

At some point, go into the microG settings and perform the self test to check if signature spoofing works. If not, it usually helps to boot now back into TWRP and to run the patcher again. Boot back into system and redo the self test.

Before you create your Google account in the ROM settings please make sure that "Google device registration" is enabled in the microG settings.

Setup your desired backends and GCM push requirements through the microG settings. If you set location to either "savings" or "high", the microG self test should show all boxes ticked. I don't have any requirement to pass SafetyNet therefore no suggestion by me at all (anyway with my current ROM/kernel I never achieved to pass the SafetyNet check unless I'd unroot what I won't do, but with Xposed anyway no chance to pass).

Setup your device completely to your desire and enjoy.

Please feel free to advise if I described something poorly and wrong. Hope I didn't forget any major point in regard to Nanomod or microG.