The recent changelog shows a number of new mechs added, yet most of them don't appear in the skirmish Mech-bay. The following variants are missing:

Grand Dragon DRG-1G
Warhammer WHM-7A
Maraurder MAD-2R
Zeus ZEU-5T
Battlemaster BLR-1GB
Crab CRB-27b
Cyclops CP-10-HQ
Javelin JVN-10A
Raven RVN-3X
Catapracht CTF-0X
Phoenix Hawk PHX-1b

Now, I've been playing around with mods (unsuccessfully) trying to add those mechs before, but after failing, I disabled mod support. Also, I own the Heavy Metal expansion, but not Flashpoint and Urban Warfare.
Should these mechs be included in the vanilla game and in the skirmish mech-bay? Or are they campaign/career only and do they need some of the expansions? And can modding attempts interfere with the new update?

These mechs, as you indicate, are missing.
They're missing from skirmish, because they have been blacklisted.
It have been done, because, in my opinion, most of these mechs use Star-League era technology, like double heat sinks, ER lasers/PPCs and Endo Steel chasis Ferro-Fibrous Armor with allow to better dissipated heat, have better range or justsave weight and allow to have moore room in mech. SL-era Griffin, Highlander and Black Knight are also missing from skirmish.
Mechs below use SL era equpiment:
Warhammer WHM-7A
Maraurder MAD-2R
Zeus ZEU-5T
Battlemaster BLR-1GB
Crab CRB-27b
Cyclops CP-10-HQ
Phoenix Hawk PHX-1b

In skirmash, these weapons and HS would give unfair advantag, if used against "normal" mechs with single heat sinks, nornal lasers and so on.
Some other mechs are blacklisted because, in my opinion, they posses experimental technology.
Raven RVN-3X
Catapracht CTF-0X
Lastly, it is a mystery to me, why below mechs are blacklisted, because they seems to fit into game technological level.
Grand Dragon DRG-1G
Javelin JVN-10A

I hope that my inforlmations have answered for some of your questions.
Best regards
Mateuszy

EDIT: I have all DLC's and can use Javelin JVN-10A and Catapracht CTF-0X. You probably cannot use them because You are missing 2 DLC's.