>>However, I feel like it's a minor issue that can be ignored while the in-video ads are implemented for HTML5.
You might not think it was such a minor issue if it was your revenue coming out of your wallet. It's not just YouTube, Google, and the advertisers that are affected, but every user with a monetized video. You're tossing all of their incomes like it's no big deal, and I'm sure they'd disagree with you.
That aside, since HTML5 is still a WIP, not anywhere near all videos on the site have even been re-encoded for it yet. Many videos simply aren't available, with or without ads. You can't "force" something that doesn't even exist yet.