Wouldn't it be easier to just have a drainage layer of large pebbles up to the height of the water level and then have a permeable membrane that would link the aquatic section and the submerged terrestrial section? That way you get good drainage downwards in the land without having to worry about water pooling up somewhere that you'll never get it out. It's just one less thing I have to worry about maintenance-wise.
yes and no. if you build a false bottom with a drainage tube, you will be able to get the water out very easily. just stick something down into the reservoir and suck it out.
the first problem with a permeable layer is how will you clean it? detritus is going to accumulate there and you have no way to get it out.
second, if you fill up water all the way to the bottom of your substrate water my end up wicking up into your substrate and waterlogging it. it will kill your plants. you would still need to have a gap between the pebbles and your soil to prevent this and a screen to stop your substrate simply falling in through the pebbles. some of your substrate will probably fall through the mesh anyway, and cloud your water.
third, you want to keep your ferts separate. depending on what plants you end up getting, you don't want terrestrial ferts leaking into the water or vice versa. for example, exposure to strong fertilizer will kill some bromeliads and tillandsias outright. i doubt anything really bad would happen, but then again, do you want to take the chance?
anyway, either way will work, but you'll have to plan it out or you may end up running into problems without an easy fix later down the road.