In general, you usually don't want to embed wood in the concrete. Some possible 'issues' that can occur would be: rot (yes, even PT can rot), moisture, and strength/depth of the concrete itself.
Let's see, most of the shop floor is a 6" thick fiber-and-steel reinforced concrete slab on grade. But somehow you have a 'room' with some PT floor joists resting right on the ground (like a shed floor) and 3/4 plywood on top of those PT joists. Pouring some concrete in/on/in-between those PT joists and then having it up at the level of the plywood floor (and thus probably touching the plywood as well) I think is just asking for moisture and/or insect problems.
And how would you excavate for the gravel underneath the concrete slab without undermining the on-grade PT joists (which are probably 'sized' for being on-grade and most likely not sized to actually have any span to them)?
If you have any pics/images in your post, I can't see them right now because they are not coming from GJ but some off-site locale and hence aren't 'getting through' here.
To me a mill and a lathe would indicate a need (or at least a strong desire) for a strong and solid floor underneath them in order to both support the machines and to support them solidly without vibration.
PT joists right on grade with plywood on top may be strong enough for many things, but I think that putting big $$ machinery on top of that type of floor is just asking for moisture issues from the ground as well as vibration.
YMMV and all this is just IMHO. I have also been accused of a wee bit of 'overkill' in building things too.
