I'm not sure the army specific bonuses are worthwhile. This is really more of a question than an opinion but my reasoning for this is that, although there's generally only a small advantage/ disadvantage to these rules, it's a bonus that's not paid for and doesn't work against everyone.
Taking the Witchhunters as an example, why only undead and chaos? Given the fanatical nature of the army surely anyone who opposes them must be riddled with chaotic corruption and in dire need of cleansing regardless of their alignment. They're not reasonable people. I think this is specifically detrimental to undead as they're just not very fighty.
I've always found the flammable rules for wood elf critters a bit on the nose. Not every army has access to fire creating spells or machines so they'll miss out. If you knew you were taking on WE then the temptation to add in the fire starters is pretty compelling.
Due to the games general balance these rules aren't a huge deal but if things went against you because of them I think there would be cause for complaint.
On another passing thought, I'm going to have a decent look through the WE rules as I'd like to get something started. Can someone let me know where I can find any version not in the Warhammer trial armies doc (one that also contains Grimgor rules).
Cheers