Sorry for delay. Could not replicate in sandbox. Issue persisted on all pages in vault containing admonition even when reverting to restricted mode. Nothing showing in console when going through export process.
I have the same issue.
I first encountered this issue using the third-party plugin, but also the stock callout blocks do get ignored when exporting a note to a PDF.
I just tested it in the sandbox vault and the issue does not occur in it.
Yet, if I disable all community plugins in a regular vault, the callouts are still ignored when exporting to a PDF.
I followed your instructions and then the callouts were displayed as in the sandbox vault.
I then switched back to the theme I use (Things) and then the issue occurred again.
So it seems that the issue is NOT caused by core Obsidian.