Can one use muriatic acid instead of acetic acid (vinegar) for syrian rue extraction?

I don't see a reason why not except for some practical reasons (vinegar is more readily available & food safe, does not produce irritating fumes, is safer to handle).

However, having a clean HCl, is there any physical reason it could not be used? Any excess HCl will evaporate and harmalas will already be in hydrochloride form when doing Manske. It seems cleaner to me as less chemicals are involved in the process. HCl also reacts with sodium hydroxide forming table salt, which is also already present in Manske.

It might work, the only problem I can forsee is that solubility of harmala hydrochlorides in HCl might be limited for the same reasons that the Manske precipitation works - the excess of chloride potentially will cause the solubility product of the harmala HCl to be exceeded.

Manske used acetic acid, perhaps for this reason.

I've successfully extracted rue with muriatic acid before, no problem.
Even went to pH 1 during the acid stages, to break cells up, but that is not necessary.
I had to use lye as a base to base it, carbonates would have to be too much of them to neutralize that strong acid.

I can't remember if I tried to manske in a muriatic environment.

there is one HUUUGE problem with hcl, imho.
extremely corrosive fumes.
i am speaking from experience here.
if you have valuable equipment containing metal in the vicinity, even in the next room, doing anything that involves using hcl in a kitchen setting is kinda stupid, imho.

^^^ Yes, I did everything in glass back then.

That's why I asked whether there is a physical reason, apart from practical reasons.

It was mostly an academical question.