Presumably, selecting the do not change option under the paragraph first line indents section of the settings of my chosen layout in the sections layouts editor in compile SHOULD allow the first line to retain indents. This does not seem to actually be the case. My first line indents are still being removed.
Additionally, when choosing the section layout that is just a page break with the following: MAIN text formatting will be based on how text appears in the editor… creates text in the compiled document in a completely different font and size.
For instance, the text in my editor is set to Times New Roman size 12 and it compiles in Palotino Linotype size 10.
Scrivener 3 doesn’t have this problem at my machine. Beyond that, all I can offer is a Zoom session to try and figure it out. You can messenger me at https://www.facebook.com/DrMajorBob.