Will you be removing the MFT? I have 2 such carts. One has shelves for sustainers, the other does not and stores other random tools (e.g. planer, TS 75, etc.). I removed the legs on my MFT's. I can reattach them if necessary.
One cart does not have any mortises or blocks or such keeping the MFT in place (at least not that I remember adding, as I built this many years ago). The other cart does have some bolt-on blocks that hold the MFT in place. Both carts put the MFT's at the same height so that I can configure the workstation as needed.
One thing I found vital with using the MFT - The MFT is small. You MUST have a space to place other things that you use in whatever your task is (e.g. tape measure, chisel, screwdriver, clamps, etc.). You will find yourself moving these items constantly. So you must account for a buffer space.
I built my carts to make use of that dead space between the top of the cart and the bottom of the MFT. The folded legs would get in the way, hence their removal. If you could mortise in the legs to the top of the cart, then try that. I don't know if I considered that at the time, but the ability to get my hands under the MFT and scoop out small things that drop from the holes (e.g. screws, etc.) is important. Having the legs in the way or mortises may make retrieving these items a frustrating task.
Don't ignore the use of that dead space. You will need it. Otherwise, you will find yourself spending tons of time "transferring" items from one space to another in the course of your task. Things like clamps, sandpaper, screwdrivers, you name it. You have to have a place to set them down, and the MFT top isn't a good place for them if you are using the top. These "transfers" are inefficient, and get old and frustrating really fast.
Due to this dead space, my working heights are not the same as the original table with the legs out. If I were to build the cart at the original height and include that buffer space, I wouldn't have much room for sustainers or a CT 22 or 26 extractor under it. So I'm not working at the optimal ergonomic height. But this was an acceptable tradeoff to gain that dead space I mentioned.
Some things to consider in your design.