This is something I've been thinking about a bit myself. 'Mechanicum', the (MacPherson, semi-canonical at best) novel, which you may have read, desribes the split of what was later to be called the Dark Mechanicus, due in part to a system wide infection of 'scrap code'. This subverted those exposed, and lead them to support the heresey. The origin of the scrap code is never fully explained or explored beyond it having being sealed away at some point in the distant past. It seems to me to be a combination of:
a) a direct link to Chaos in a machine specific format
and/or
b) a form of logic or code that was introduced and utilised by agents of Horus to subvert the Cult to his view, but being one or more steps removed from a direct Chaos origin.
It is also possible, although not mentioned in the text, that this is either an older/ancient code or logic that was rejected by early Cult members as an antithesis of thier beliefs, or considered heresy and deliberately sealed away with associated technologies. This would suggest to me something akin to Cult members finding a source of A.I code and hardware; very attractive to a minority, reviled by the majority and something that could possibly escape its confinment and become a 'techno-plague'.
A specific source within the Chaos pantheon is never mentioned, and whilst Tzeentch is one of the more likely, it is equally possible that there has always been a 'Dark Omnissiah' lurking in the empyrean.
As for Dark Mech. symbols, I have not seen anything agreed by any number of people except that some shade of purple is favoured over red. As for abased or desecrated cog sysmbols, I have yet to find anything hinting at that or an alternative motif.
I personally think that it is possible that a part of the Dark Mech. actually views itself as the true channel of the Omnissiah, and that all others as heretics, so would continue to use the unaltered cog and skull. Others may use altered colour schemes....maybe something like the black and yellow of the Iron Warriors instead of black and white.
Given the lack of specific canon, I think your pretty safe coming up with whatever you think looks good, since the Heresy there must be countless off-shoots, sub-cults and so on.
As for your background, I think its very apt, and quite likely, that virtually any Explorator party is going to be far more interested in what new technology may await discovery than a minor inconvienience like being sealed under a planet.
I do agree with Allod that a direct manifestation is possibly a step too far, its equally likely the band changed thier views through being sealed in by a traitorous heretic/advanced radiation poisoning/an internal coup in leadership/madness/exposure to lost technology etc, etc.
Whatever you decide, I'd be interested to hear more...
Edit - wrongly attributed authour and misspelt novel title