Bitcoin Core don't care about file system, so i doubt exFAT is the problem here. I've seen some people use FAT32 or exFAT on their external drive to store Bitcoin Core files without problem.
Have you consider you might fell into XY problem? For example, if you just need to get recent block and your user don't care about privacy, you could just use few free API offered by block explorer rather than obtaining data from pruned Bitcoin Core.
I wanted Bitcoin Core to be stored on a USB with BTCapsule, but I changed my mind. It wouldn’t make sense to have an old version of the software, and it was causing way more problems than it solved. I don’t think asking someone to install Bitcoin Core themselves and add a few lines to the bitcoin.conf file is too complicated. Hopefully it will lead to more people running a full node. This is what I’ve been working on:
https://bitcointalksearch.org/topic/btcapsule-is-now-free-and-logs-year-from-bitcoin-cores-mediantime-5417348