I’m using a .ipynb notebook as source for my Vignette, so I created a Vignette engine inside my package to build it.

That one registers a the necessary extensions, and R CMD build obediently creates a vignette from the .ipynb file.

Yet R CMD BiocCheck still says REQUIRED: vignette sources in vignettes/ directory. should I ignore that when submitting my package, or will the bioconductor people have to fix that check beforehand?

BTW, questions about package development and submission should go to the bioc-devel mailing list.

We don't yet have a policy about .ipynb vignettes and we'd have to make sure the build system is capable of building them. However, I would ignore the error for now and you can discuss it with your reviewer when you submit the package.