There is no difference between the two boards apart from the extra slots as you say, just depends what you use. My Mediator Lt houses a graphics and sound card, network card and spider USB. A word of advice is that the graphics cards are difficult to purchase in PCI form so make that your priority before you purchase your Mediator.
In terms of towerising your Amiga the D Box and the mediator fit like a glove.
In answer to your last question yes an accelerator can still be used.
You will not be disappointed if you go ahead with this upgrdade.
:-)