Have a look at my Colemak[eD] if you will (in my sig topics): I felt the same as you about dead keys but at the same time I need dead keys for accents (yes, I actually use them as I love languages). So I decided to have both a non-dead and dead version of symbols like tilde and caret! That way I get both the power needed for advanced typing and the ease of access needed for coding. If dead keys are hardly in use for others, they could always swap a few lv3 mappings with the lv4 ones (since dead key usage is a bit tricky I've elected to keep them on lv3 mappings for my own purposes).
Don't sweat the positions of those out-of-the-way keys, is my suggestion. They really don't affect your typing speed and the only discomfort they really cause is in your mind when minding them. They're not used that often so being out of the way a little is just fine - you just need to practice a little to feel comfortable with them. This is why the standard Colemak doesn't mess with the positions of those keys, it's just not worth it (arguably the hyphen could've been better placed, I agree, but I chose not to change that either and with the Wide mod it's fine for me at least!).
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