Creating /storage/.config/samba.conf will not cause a boot failure. That code is relatively unchanged since OE 1.0 days and we would see thousands of forum posts if it were true. The boot message says it cannot find the SYSTEM file in the boot partition (first partition of two used by LE) which is normally because some other process messed with the bootloader config so the partition is wrongly identified or the file is not present or corrupted (cannot uncompress).
I've also tested this out now that I'm not on vacation and (sorry) it doesn't work quite as expected. It's not blocking creation of a directory; samba docs only talk about blocking files so it might be that explicit. Also, blocking a Thumbs.db file that I copy/paste prompts macOS/finder to ask for credentials instead of the copy operation silently failing. It may be easier to let Android do its thing uninterrupted and just run a regular find/delete command via cron instead.
NB: In MacOS you can prevent write of _ and . files: Mac OS X v10.4 and later: How to prevent .DS_Store file creation over network connections - Apple Support so no need to do that with Samba