How to Sync MacOS Applications + Preferences across multiple Macs without OS X Server?
Seems like ChronoSync could help in a limited way. The support pages have warnings on syncing ~/Library. See ChronoSync - Syncing your Home folder.

You could try Unison for everything instead of multiple tools and approaches (one caveat is that Unison was last updated in 2009; it's source is available under GPL though).

References:
Unison Frequently Asked Questions (FAQ)
Using Unison on Specific Operating Systems