I've tried an initial modded run with a couple of mods. Took Hegemony commission, got to Sentinel cache and asked the fleet to move. After returning some time later I found out that, in fact, only Legion is actually an automated ship here. Other ships are entirely different: no s-mods, no d-mods and not automated (despite actually being piloted by cores).
Modlist (everything latest apart from lunalib (one version back) at the moment of initial discovery)
Spoiler
{"enabledMods": [
"$$$_trailermoments",
"lw_autosave",
"chatter",
"lw_lazylib",
"logisticsNotifications",
"lunalib",
"MagicLib",
"wisp_NeutrinoDetectorMkII",
"stelnet",
"zzz_DakkaHolics",
"ShipCatalogVariantEditor"
]}
And how do I send the savefile? / What do I do to provide more info?