Stone to Flesh can target a “ human-size stone object,” and a Wall of Stone is way larger than human sized, but Wall of Stone provides that “Each 5-foot-by-5-foot section of the wall has AC 10, Hardness 14, and 50 Hit Points, and it's immune to critical hits and precision damage,” so I don’t think I’d be out of line treating each 5 foot section as an object. The volume is the average human is about 3,783 cubic inches. The volume of a single segment of the wall is 3,600 cubic inches, and that looks close enough for magic.
So my thought is that Stone to Flesh affects a five by five section of wall, transforming it into “a mass of inert flesh (without stone's Hardness) in roughly the same shape.” At that point, I assume it could just be knocked over, but if someone wanted to damage it, I’d just use the Wall of Stone stats minus the hardness.
The question is does size mean mass or volume? Depending on the density of the stone you could have 2 or 3 times the volume of flesh. Since you have to get in touch range you would then end up covered in a mess of flesh and blood! That's just unsanitary! Please use stone to flesh with extended range metamagic!
More seriously I could see how the spell might fail unless the whole wall is 5 by 5 because the wall is the whole object, but... I would probably play it they way the OP is reading it, because it is a 6th level spell, stone shape is 4th level and can get you past walls. I also don't know why else you would use the "turn a stone object into a mass of inert flesh" unless the flesh has particularly good culinary properties.
In classic editions, the spell was used to burrow holes in stone by some of the game makers, so there is a precedent.
The trouble is, can you target a portion of a whole?
I'd say usually not, so no more tunnels, except Wall of Stone seems modular, having stats for each section.
I'm still leaning "no" since Flesh to Stone seems to have rigorous limitations purposefully in PF2.