The differences in the weapons can be attributed to them having different armaments, with the Thor having UAC5s and the Loki having Gauss Rifles and Large Lasers. Being OmniMechs, this shouldn't be a very big deal, it would have been easy to magnetize too if metal models weren't so heavy. I'd chalk up most of the differences to it being a 2D drawing with attempts to make them look more dynamic, the exceptions being the pistons above the knees on the Loki and the groin area, which I believe there are some very simple solutions for - namely having the option to assemble the groin either way, with the back representing the Loki and the front representing the Thor. I vaguely recall some Clickytech models doing something like that, though that might just be genuine Chinese quality.
As far as staying true to the art is concerned quite a few of the recent miniatures are far more plain than the illustrations they were based on, an example being the Dragon II's cockpit. Doesn't make it any less of a cool model and a great replacement for the classic Grand Dragon, likewise if your Thor II doesn't conform entirely to some flat piece of art it won't degrade the overall appearance as long as it is consistently done well and the casting is on the mark - I'm going to spend more time looking at a tabletop model than any TRO art. I've been painting 3 Jenners recently, and I'm hungry for something new that doesn't look quite so downtrodden and miserable.
Still, with the whole point of OmniMechs being modular bits it would be pretty silly if at least the weapons for the 2015 Thor II and 2019 kickstarted Loki II weren't to be compatible, even if the latter is cast in hazardous chinese resin by trained mongolian cat-monkeys imported from the far east, or far west if you're on the west coast.
Again, I'd also expect the initial costs to be cheaper if you recycle existing components, which would increase the likelihood of the Loki happening. As this is not the case, well, guess I'll have to stock up on epoxy and plasticard.