A few notes:
Killing a mob below EM doesn't break the chain, though it will usually take time that will cause you to miss the next chain. Beastman BST pets are usually Easy Prey, but they go down fast enough that they don't cause chain problems.
The pet penalty only affects BST, not DRG or SMN. It is applied before the base xp cap, so it is possible to get 200xp with a pet if you're fighting VTs solo.
Perhaps what the Brady guide was actually saying was that if the BST charms a mob of a higher level than anyone in the party, the pet's level is used to calculate the base damage. This is true, so having your BST charm an IT and use his 2-hour to keep it charmed isn't good for the xp (though it's very useful for quests). Too bad they didn't make this clear, so people think they were talking about the 30% pet penalty. ><
An alliance of two parties of two characters should in fact get more exp than a single party of 4.
And a recent change: The CoP patch raised the base xp cap so 51+ can get 250 without a chain, and 61+ can get 300.