Trying to answer your question, you may use PCB mounted switches that will give you the easiest top removal option, unless you install in-switch LEDs, that should have dip sockets if you want to still remove the switch tops. If you want to go the plate route, you should take care of getting a plate with notches to allow switch top removal. It will not be as easy as with PCB mounted switches but it is doable. If you want to make small changes in the layout, the PCB mounted switches is the best option allowing for full freedom regarding alternative layouts, the only limit will be the PCB itself, plates will have a bit more limitations than PCBs alone; but, still there are "universal" plates that allow some options. Sixty keyboards are the niche that offers more options regarding PCBs and plates, followed by TKL, full size customs are not that popular.
The final overall feeling and sound of your keyboard are multidimensional responses, where the factors are at least, the case, the case's feet, if any, the plate, the PCB, the switches, key caps installed and even the surface you will put it on to type. Their materials, thickness, final weight, to mention some of the basic ones; therefore, there is no single factor that drives the entire typing experience, so the PCB vs plate mounted option is one important aspect of your build, but it cannot define the entire thing by itself.
As most fellows, you should take on your quest in looking for the best setup for your needs and likes. Again, the options ranges from plastic to metal cases, aluminum and steel plates, cheap and expensive PCBs, cheap and expensive key caps, multitude of switch options, colors, stems, springs, just talking about MX; but you may consider ALPS, because BS and Topre are not that customization friendly. Good luck.