On some very large industrial rigid frame structures that I have seen (high eave heights, and heavy crane loads), and where floor trenches/pits are a factor or could very likely be in the future, a foundation with a pair (or more) of piles in line with the frame/truss span have been used. These piles can be very large, sometimes with bells to resist uplift effects, and in some instances I have even seen battered piles to resist the horizontal loads.
One key thing, if you use ties through the slab, make it clear on the drawings that this is a critical part of the structure design, and that removal of the slab, or cutting (say a trench) across a column line requires consultation with the engineer prior to construction. This at least would protect you from the future owner who say decides to remove the entire slab for some reason, and maybe even replaces it with asphalt paving. If this happens and there are problems with the structure down the road (perhaps not a collapse because passive pressure against the grade-beams/foundation walls may provide some level of lateral resistance), but certainly serviceability problems (a binding bridge crane for example), then you as the designer-of-record should be off the hook for problems caused by this owner, because you made your design concept clear on the drawings.