I think there is a conflict because magisk replaces init, and my 2ndinit replaces init, and it looks like I have a hardcoded call to SuperSU in there, as well. In theory, Magisk might work on everything, but it would be very tricky. So for starters, if you disable the boot menu, does Magisk work?
I have no clue if this is going to work, but it should. Starting from the 5.2.6.9 zip, you'll need to remove from META-INF/com/google/android/updater-script everything between these 2 lines (including these 2 lines):
ui_print("Installing recovery...");
set_metadata("/system/app/SuperSU.apk", "uid", 0, "gid", 0, "mode", 0755, "capabilities", 0x0);
Flash that, and verify it boots and everything works. You should not see the bootmenu. Then boot in to recovery with adb and flash Magisk and see if that works.
Alternatively, if you dont want to edit the updater-script, this is less clean, but should product the same results. Flash 5.2.6.9. Stay in recovery. Ensure /system is mounted. In adb shell, run these 2 commands:
rm /system/bin/e2fsck
mv /system/bin/e2fsck.real /system/bin/e2fsck
Exit adb shell, make sure to unmount system, and then reboot.