Those holes you talk about filling in and closing up. Arn't they for for what I'll call the idle air bypass? The earlier tq's had a slot or channel in the bottom casting. This routed idle air into the intk bypassing the butterflies and the idle circuit. The later model brings that passage up to the top casting to where you have shown.

I normally open up the idle jet (idle feed restriction) to richen up the idle. I reasoned that blocking the idle air bypass would mess up the throttle blade to transfer slot position at idle.

If you have more thoughts/info on this, please share. I'll try to post a picture of the earlier model idle air bypass.