I solved this via "unconventional" yak...
This is why I opted for a feather-light, small inflatable yak. That and my love of the bayside flats. If the yak is light enough to carry for long distances then it expands the time frames dramatically. It pretty much eliminated all of these timing considerations. I most likely increased my susceptibility to wind though, but since I am not using this as a trekking yak I can probably just get out and walk back to the truck. I won't be making any open water crossings, this is purely a flats shuttle.
Paid my dues...
I used to lug a 16 foot fiberglass canoe to fish the bayside flats for years. It extends the fishing time a lot but it's too much for one to carry. It is also difficult to get into once you have stayed on the outer shoals too long - but that's where all the big cows hang out. I learned my lesson from these excursions.
But to answer your question...
You are best to go out with a tide and ride the flood back in. The earlier you start, the less you have to worry about dragging or lugging. The later you return, same. And then there's wind.
By choosing an area that has a channel w/ flow thru the low, you will be able to reduce or eliminate the drag factor. This can backfire if you hope to return during the outgoing tide, the currents will multiply your effort returning to port.
Typically, the more you want to fish the flats, the more you dry sand you face. Therefore the ideal location to launch would be a channel right next to a parking lot that holds water thru the low with slow current speed on the outgoing that leads out via a short paddle to some great flats where you can get out and get in the yak easily. When you find that place, please let me know
In the mean time I have a suspicion I will be quite content with throwing my inflatable over my shoulder and high-tailing it out to the Blue Hole across .5-1 mile of sand, way more than I would care to drag.
I refrain from keeping a 20# bass out there because of the drag back to the truck, never mind a 80# boat