Mixing clean and effect channels will ALWAYS have tone changes from phase issues. There will always be some overlap of waves, either boosting or cutting each other depending on the overlap. Changing the volume of one of them changes the intensity of the cut/boost.
There are tools for addressing phase problems: FEA's mixer pedal offers full adjustment between 0 and 180 degrees, and some blenders (e.g. by Xotic or Badger) have a simple 180 degree phase switch. Of course how well these work depends entirely on the specific effects being mixed, and their settings.
Also, in your system the sound will always change because your clean channel is at 100% volume at all times, while the effect channel goes up and down in volume. So the more effect channel you fade in, the louder you will always be.
Yes it is possible to make a box that works better or sounds better than the Boss. You could talk to [sfx] www.sfxsound.co.uk
about a custom project like that, as he specializes in super high-fidelity utility pedals.
But I'm not sure how much of the "sound changes" you are unhappy with are due to the Boss, and how much are due to the nature of what you're trying to do.