I’d like to break chapters into multiple subdocuments without page breaks appearing between them on the ouput of the master document. Is this possible?
There is no reason for a page break between subdocuments unless you put one there (either at start of subdoc or manually between them).
If you want predictable and reliable formatting, I highly recommend working with a common template so that styles are consistent. What is your styling habit?
For more ad-hoc help, give more details on your present document structure, notably how you mark up chapter headings, sub-chapters, etc.