Let's say I own game A, B, and D, and Steam has a package on where Games A through Q are bundled for a price attractive enough to justify not getting "as good" a deal as someone who owns none of A-Q.

Is there a way using the Steam inventory, or some other method, where I could buy bundle X, containing A-Q, activating C and E-Q on my Steam account, and having A, B, and D available to trade/gift in the future?

Not always. Sometimes the package deals are sold as a single tradeable "item", usually when it's a franchise pack of sorts.

Nope. Not for the majority of games at least. Certain packs do provide you with extra giftable copies of owned games, but they're rare.

Steam only provides "giftable" inventory items of Valve games you already own.

So, if you buy the Orange Box but own Half Life 2 already, you get a giftable copy of HL2. But I don't think any other developer/publisher has agreed to do this on Steam. Generally most people don't seem to mind since the bundles tend to be very good deals.

In 99% of cases... no

They really need to fix that. I could see lawsuits over that, as you are not receiving what you paid for.

I wanted to buy the Total War set, but all I need is Shogun 2. The package is a great deal, I would have bought it if I could gift the other copies. Oh well.

Why "fix" ? One person cannot own two same licenses on steam. It's in the TOS - one license per person.

GOG gives giftable copies, because GOG is awesome, not because they have to.

Here's the official Steam page on "extra copies".

https://support.steampowered.com/kb_article.php?ref=4502-TPJL-2656

If it quacks like a game retailer, it's a game retailer.