[Google Pixel 7 Pro] simplepinoi177:
Glad you got it working and figured out! I imagined it was the emulation. Using the newest platform-tools is probably a good idea (there was a circumstance it wasn't for a while there, but apparently that has passed).

That's curious about the file manager crashing -- I would force close & clear cache on Magisk, make sure it has all the right permissions (permissions for files & folders) and if it uses the stock AndroidOS file explorer you might want to force close and clear cache and data for that as well (you'll have to re-set up the few settings/customizations for the file explorer app if you clear data). If that's not enough, maybe uninstalling Magisk Manager app and re-installing it.

If you look under Run Xposed Check, the last entry at the bottom that states "Magisk Random Package Name:" will show any Magisk remnants from "Magisk hide" or other Magisk instances; outside of the main installation.

If you did find something odd -- meaning random characters (mine for instance is "bb.oufsahvt"; I believe there's always a period after the second character) that Magisk hide renames itself -- or other Magisk instances, usually you can find it in your App Drawer or "see all ### apps" in the Apps section in Settings . There might be ways to go about finding and/or removing if you can't find them that way (I imagine adb commands), but I've never been in that situation to learn about it and/or am unfamiliar with other methods others have used.

Yes, it's one of the top most helpful tools (for Pixels and some others) established! It's able to do most anything you'd want to do with flashing and rooting!

This makes me further believe that you are running two separate Magisk instances -- the fact that PixelFlasher produced a unidentical patched file. PixelFlasher may employ different methods, but it normally runs code to simply use the Magisk already installed on your phone -- so the patched file is a direct product of your specific Magisk -- so that's why I find that real peculiar. PixelFlasher (PF) actually has other methods like where you can emulate an external instance of Magisk to patch and what not, but it's not default and you have to "Manual"ly execute it, or using script on the "core Magisk" in the root directory, or other methods. But none of these sounds like what you did, so it shouldn't come up with a different patched file.

If you are very curious and wish to get to the bottom of the mystery, create a support file, post it in badabing2003's thread and mention/ping him, and he'll take a look and see what might be the reason -- again, I'm betting he's gonna come back with you running two different Magisk instances (one that PF uses and one that you had been using).

It is definitely as good as it appears to be, and probably been even more. I will leave you with a couple quotes below on other members' views on the program and its developer (badabing2003).

But before that, I'll answer the other parts of your question, as for "always check 'Keep Data'", for the most part yes; unless you intend on factory resetting the phone and/or, in the case of custom kernels, as disabling verity & verification requires a wipe, maybe you do not check this (I'm uncertain how badabing2003/PF goes about disabling that and if it automatically factory wipes or one must do it oneself [EDIT/UPDATE: Apparently badabing2003 just released an update that does, in fact do this {source}).