One weird feature I found while experimenting was that giving a Military Base to the Holdout Forgeship allowed access to otherwise more restricted ships such as the Remnant Class types when having a high relationship. Could be useful for additional quest/mission to further assist the DustKeepers late game ? [Potentially salvaging from a domain mothership or remnant battlestation to further enhance the Holdout ie:expand colony size = larger defensive fleet].
I've some plans in the area but the next major update is likely to be more Sierra-focused - I do have an important Dustkeeper quest iceboxed, though. That the colony sells only Proxies openly is intentionally to give the impression it's a band of isolated holdouts with limited resources, but you can source most Remnant ships from Inadvertent via his custom production contracts.
Re: Dustkeeper colonies - Transferring colonies is intentionally turned off because I think a Dustkeeper-controlled but human-occupied colony would need to be some kind of special event with special mechanics.
Re the rest: yes they're hostile to Derelicts and Remnants, there's not a breadcrumb leading to Mia's Star yet, and beta cores mostly don't do anything in Holdout and are there as a fun lore thing (canonically, gammas get sent to war, betas go in logistics processing, and alphas get to sit in a nice comfy box). AFAIK it does not affect Colony Crisis activity in any way, as Hegemony crisis only counts player colonies for AI point progress