If the bibliography error is the main issue, there is How to share bibliography in a multi-file setup? - #9 by PgBiel and some workarounds identified.
Edit: Since Typst 0.15 now allows multiple bibliographies per document, adding this to your #include files should do the trick:
// chapter.typ
#show bibliography: none
#bibliography("references.bib")
This lets chapter.typ resolve its citations when compiled on its own, while hiding the additional bibliography when it is included in main.typ.
However, this does not answer the original question of whether a Typst project can declare which file should be treated as its main/root file.