This isn’t something Scrivener is doing, that is how the MultiMarkdown engine (and Pandoc as well, if that is what you are using) handles ASCII punctuation by default. These tools have flags that can turn that behaviour off if you want, and Scrivener v3 now gives you direct control over the command line (to the extent that you could even use another conversion engine entirely if you wanted).
Firstly, I would suggest installing MultiMarkdown on your system. After you restart Scrivener it will pick up on the installation and use it instead, but that is more of a side benefit. It will make what you need to do next easier. The procedure is described in this thread. There we explored how to set up a custom MMD command line to switch off the automatic IDs it adds to headings, but the same basic approach would be used to customise the command line so that it doesn’t use smart typography.
The documentation for MultiMarkdown’s command line arguments has this to say:
multimarkdown --nosmartDisable smart quotes (e.g.
"foo"does not become“foo”).
(For Windows, you of course need to address the software as multimarkdown.exe, and it is best to use full paths in the Path field, like C:\Program Files\multimarkdown\multimarkdown.exe, if that’s where you installed it.)
In Scriv1/Win, of course, there was “straighten smart quotes,” “convert em-dashes to double hyphens,” and “convert ellipses to triple period” under Transformations.
That wouldn’t ever have changed how MMD works though, they change the .md file that Scrivener creates before handing it off to MMD for conversion. Giving it straight quotes allows its engine to handle typography, which it will generally do a better job of.