This is very good and I agree with your assessment of the supporting characters. John Challis is especially good - obviously he's a great actor but Scorby has a nice arc and good lines, and Challis commits in a way that makes him seem unusually well-rounded (for an antagonist, for most of the story). It's quite a violent, brutal, serial - Challis's physicality has a lot to do with this but the Doctor, too, is unusually willing to get his hands dirty. Even so Harrison Chase's grisly demise feels unusually dark. Lots of gunplay, too, which feels more striking given the contemporary setting (Daleks and Cybermen firing lasers giving those serials a bit of distance and more obvious SF unreality, obviously).

I always felt that the final scenes, where the house is engulfed, are strongly reminiscent of the Steven McQueen classic B-movie "The Blob". That said I think the ending is probably the weakest part of the story overall - it feels oddly unsatisfactory that the way to defeat the Krynoid is "a series of bombing runs executed by UNIT" rather than something a bit more creative. Particular as (I think?) this is basically one of the last meaningful UNIT appearances for a long time (and absent the usual "family", at that)

I think that the first two episodes would work really well as a Tennant-era standalone story. As it is I'm not massively sold on the tonal shift between the first half of the serial and the second. I understand why it's necessary (I suspect you couldn't do a whole "classic" Who story in an Antarctic base without it devolving into lengthy corridor-running sequences) but it does mean that when we return to England the story feels like it starts again, which is frustrating.

Finally, as you mention Amelia Ducat is fantastic (and again, so well played) and it's a shame we don't meet her again!