Set up your text variables as running header character styles… then reference them in that manner.

https://helpx.adobe.com/il_en/photoshop/using/actions-actions-panel.html

if you really don’t want this behaviour then rasterise your graphic and save it as tiff and important to Indesgn

1. Your story direction should be RTL
2. Your paragraph direction should be RTL
3. You should use a typeface that is befitting the subject matter, if you want a free one – maybe EzraSIL
4. Your diacritic position should be OpenType (positive adjustment is up)
5. Who chose the column width?
6. I’m still not sure where you’re sourcing your text, here it’s Genesis 1… I took it from another location and the issues you face are not there. Maybe try https://mechon-mamre.org/dlt.htm (my source is not free – but this is).
7. the fact that you say that you “think it is caused by the nekudos” is probably because your text actually has (as I suspected in an earlier response) characters that you are not seeing (and not the nikkudot).
8. Work on your justification settings and the verse markers (and onwards with your peticha and/or stuma later).

How did the text get into DavkaWriter!!!
Open it in the story editor and chick’for characters you don’t need.
Go to sefaria.org and Fontbit.

I design books in Hebrew and am curious about your claims because I’ve not come across it.
Screenshots might help and more information.

InDesign treats them as embedded vector EPS files (although you can’t “unembed” them).
You can create a QR code, export to PDF, open in Illustrator and save and/or copy/paste the vector into InDesign (obviously scanning and checking it for readability).
Alternatively, use a dedicated QR program or service to create them.