George,
dont puree it. i feel it would be a step change too soon (too many variables being changed at once).
just give it a stir then taste the liquid. agreed not ideal.
once stage 1 cook and blended then no problem tasting during the stage 2.
i have tried the stage 2 before and confident things dont improve past 20 mins once brought back to the "boil" (simmer for me). think i went upto 7 hrs (posted some time ago).
it's really in the stage 1 cook that i'm intrigued on - due to the various descriptions used of the end point. for me mushy onions but not any smell or "vinegar" etc. its if going past the mushy stage or as Secret Santa says giving it heat - does this produce a better base.
i feel that your slow cooker approach is hopefully like putting it all in slow motion. pure guess and may be wrong.
best wishes and fingers crossed