ran a few more tests because i realized it wasn't as simple as Omnimatter+cargo ships=crash. Disabled all mods and started with:
1) Angels[refining, smelting, petrochem],cargo ships, flare stack, omni[lib, omnimatter], RSO = OK / no crash
2) added factorio world. result: OK.
3) added Bob's[lib, assembly, plates, ores, revamp], yuoki = crash
4) removed yuoki and bob's[assembly, revamp] = crash
5) removed bob's ores, plates = no crash.
working theory: when angel's refining, smelting, or petrochem detects bob's ores and plates, changes something that results in cargo ships throwing an error if included in that configuration.
6) disabled angel's smelting and petrochem and re-enabled bob's ores and plates. result: no crash.
7) enabled original set of mods (most mods in current testing environment) excluding angel's smelting and petrochem. result: OK. no crash. 115 mods loaded.
8) disabled all mods. reset environment to only include: bob's ores+plates, angel[refining, smelting, and petrochem] cargo ships, RSO. Result: no crash. ugh.
9) added bob's[revamp, assembly], yuoki, and FactorioWorld. result: no crash.
10) added omni lib and omni matter. result: crash.
"failed to load mods: error in assignID, autoplace-control with name crude oil does not exist. source deep_oil (resource) mods to be disabled: cargo ships, rso-mod"
11) disabled all mods. reset modlist to include only cargo ships, omni lib, omnimatter, RSO. no crash.
12) enabled bob's library, ores, and plates. no crash.
13) enabled angel's refining. no crash.
14) enabled angel's petrochem. crash.
final list of fewest-mods that triggered crash when combine with cargo ships:
Angel's refining and petrochem , bob's ores and plates, omnilib, omnimatter, RSO (and cargo ships of course)
note: also tested without omnimatter but with petrochem and that was able to load. (angel refining, petrochem, bob's ores&plates, rso, cargo ships is fine) adding omnimatter to list triggers crash again.
cargo ships can load with omnimatter if petrochem is removed.