I can't say that this is bad idea in general.
Might be it will work well for someone, but not for me.
The reason is ergonomics.
For me ergonomics it's when there is no need to move hand to do something, and everything you need is already "under your hands".
For example, I'm using mouse emulation in TMK.
There is layer-tap key for layer with mouse keys and actions.
I use "D" key (in terms of QWERTY) to tap this layer.
This key is on home row and there is no need to move hand to get access to mouse keys and actions, which are located on right hand (H is for left button click and JKL; for movement Left-Up-Down-Right).
As you see, they are also on home row.
So, to use most often actions - move and click - there is no need to move any hand.
Of course, mouse emulation in TMK is not very comfortable, it's not for designers or photoshopers, it requires some time to get used to it...
But for everyday use it's enough for me.
When I need more - there is usual mouse and T650 near to me.
Compare this with touchpad.
First of all, there is no place to put it into keyboard such as Ergodox or Kinesis.
Well, actually there is lot of space where it will fit by size...
But no one of these places have any relation to ergonomics.
Wherever you'll place it, you'll must to move your hand to use touchpad.
As for me, this is very, very bad practice.
And second.
Why do you want to use touchpad at all, and which kind of actions you can't do with keyboard?
After some thinking on second question I realized that most of time I use mouse in browser, and very rarely use it in other applications.
After this I tried to use Vimium, and now I use mouse once in an hour.
And compare this with trackpoint.
It's small and you could put it whenever it's comfortable for you.
Firmware could be modified to select appropriate layer right when you strat using TP, so you'll have TP on one hand and all 3 mouse buttons on other (for example).
There is no need to move your hands, and everything is under your fingers.
I didn't tried yet, but this
have to be both comfortable and ergonomic.
I hope I answered to your question