The whole point of it is to cover all the end grains. This done on corners with mitered corners on end trim which protects end grain as a butt joint would not do. End grains on even 1/2" Ipe will allow more moisture penetration into the wood leading to greater expansion and contraction, i.e. working of the wood against the epoxy base.

I found on my 1/8" epoxied down teak deck that such expansion/contraction happens as well. This was also alluded to in an article in Epoxyworks mag a few years ago on their "teak veneer decking laid in epoxy.

Your use of flexible material in the gaps of your 1/2" veneer will work better than anything solid, I'm sure. But, end grain exposed wood may well expand and contract more than your fill materials ability to stretch and contract and maintain it's watertight relationship with said end grains of wood.

All this is if I understand your design considerations as regards trim.