Is there any advantage to different file systems on microSD?
Is there any advantage to formatting them in any other format?

There is no advantage of one over the other in terms of speed, reliability, or (as you put it) &quot;safety.&quot;
As far as speed goes, the fastest SD card isn't even close to USB 2.0 speeds so your USB port won't make any difference.
As to format, it's more for convenience; ExFAT allows the highest degree of transfer-ability between platforms.  JHFS+ gives you the best compatibility with macOS as NTFS will do the same with Windows.  It's all a personal preference.
Recover-ability (of data) has more to do with whether or not the card can be physically read or not.  Data loss on SD cards is either due to the card failing or the device glitching causing data corruption.  If the card can be read, your chances of data recovery are good.  If the card failed, no software or file format would overcome a physical failure.

Specifically looking at safety as I've lost files on another microSD that is using exFAT.

You need to look at a different technology.  SD cards are notorious for failing, thus the dual slots in DSLR cameras (or the very regimented backup workflow).
SD cards have their place and work wonders when used as designed.  However, if you're using this to augment storage in someway, you need to look at a different solution like an external USB 3 SSD drive or a Thunderbolt drive/array