ב"ה

The beastmaster can re-attach the marker as much as he wants, so the survivability of the creature is not very important. Many big creatures will be ignored by the opponent. In that case, the 3 extra life does not matter at all. Pet birds are extra annoying to kill if you don't have flyers.

So it is either 5 mana for the big creature, or 2 mana each time he kill a pet bird. The bonus will last on the big creature at least 2.5 times more, so it is worth at least as much.
And usually the pet token is what makes the difference between "must be destroyed as quickly as possible" and "too big to focus down" for 4th level animals (or at least makes focusing them a weaker move). At least that is my experience with this type of books and with wolves books (petting the redclaw alpha proved the most efficient so far in wolves books).

Your preference can be what you want, but you are utterly wrong on the statistical side I'm afraid, and provably so. On a L1 creature you will end up doubling it's damage and survivability, versus a much smaller incremental change on say a Grizzly.

Now that is totally wrong about the damage, the multiplier doesn't matter, and it is actually better to make big attacks even bigger.
when it is either 5 dice attack an 6/7 dice attack with piercing +1, or a 4 dice attack and a 7/8 dice attack with piercing +1, there is no armor value that makes the first option deal more damage on avarage, and there are some armor values that make the second option better (the only cases they are the same are against 0 armor and against resilient).

ב"ה

Some slightly-better-than-I-counted-on rolls later and my hydra was dead and the Zombies came for me next. Oops!

Yea, it happened to me as well. I played 5 times against zombie necromancer, 4 times I won and in the single time I lost it was about the same story (with a wizard counting too much on his hydra).

About

You also get more bang for your buck making a bird a pet, rather than a grizzly...

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Totally wrong:
1) On a big creature, the melee bonus is used more times as he survive longer, the life bonus can sustain more attack since he has more armor (or defense if crevere or makunda) and the armor is used against more attacks since he has more health (with the armor bonus being an exception, since the additional armor to already high armor is less effective against small attacks). It cost more exactly because it pays more.
2) If my opponent didn't bring an anti-bird counter by turn 3, he is probably going to do so by turn 4 (and if not, he will probably lose anyway). Out of the big creatures I have in my book, I bring the one most fitting to the situation (for example, if Idol of pestilence is out then I would probably prefer a mountain gorilla if I have one). So I prefer to put my extra investment (the pet) on what my opponent is least prepared for.

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It seems a bit similar to a zombie book one of my friends often play. With a straywood beatsmaster, I bring raja's fury and ring of beasts on turn 1, and then start to summon Thunderift Falcons (AKA birds) and some other creatures. His book is more resistant to birds, since he had already faced this tactic, but he didn't win my straywood with his zombie necromancer yet. The only non-pet zombie that could actually guard your mage if his bloodthirsty ability doesn't force him to attack is the zombie brute, so this book is really really bad against bird swarms.
Every straywood spellbook I build include at least 2 birds, even if it is a wolf book (and many of them are wolf books), because they are really cheap to put in the spellbook and they are usefull in many cases.

Basicly, no matter which mage you play (except for another necromancer), a necromancer must be rushed since otherwise he become too strong to stop (especially zombie necromancers). Luckily, necromancers have some difficulties standing against a rush, as he is the only 32 life mage that doesn't have a special ability that grant's him defensive capabilities (a pristess gain life while healing, a wizard have voltaric shield and forcemaster have deflect).