No. When making a slot between planes, commit to it.
Presumably, that isolation is required for high voltage reasons (some kV surge immunity?), and good luck achieving enough creepage and clearance with ground underneath it, while also using vias and thru-pads in the usual way. Or, put another way: with design rules set up properly, go right ahead, almost nothing will be able to fill anyway. Or, maybe you could pull it off, maybe the isolation requirement is more modest in the design, no idea, but there is another (if less strong) reason: might as well keep capacitance low, so that you can control total capacitance by way of "Y" caps.
Handle CM EMI with traditional means: minimize DC-DC capacitance if possible; add Y-cap; CMC and another Y-cap if necessary; if application can't tolerate much if any C (e.g. gate driver), don't bother, and find other means to solve EMI.
EMI might also be irrelevant anyway: for the gate drive example, they're already swinging at 100s of V -- your EMI filtering belongs elsewhere -- namely, prevent it going up the mains input, and thoroughly (RF) ground the main board so the EMI current across the DC-DCs' capacitance can be sunk effectively.
There's dozens (hundreds?) of possible applications that fit your outline, so I cannot possibly say which set of solutions applies; I don't even know what if any EMI concerns (converter emissions, required equipment level, and how energy is coupled from the one to the other) you actually have; for all I know, this is just a generic concern and not actually motivated by any requirement at all.
Tim