To choose no laminate top, you need to select a solid body and then just don't click on any laminate options; if you do click a top option then you can switch back by choosing 'No Laminate Top', the very first option on the top of the list of laminate tops on the 'woods' tab. If you're seeing a laminate top selected in the builder with a solid body then that means you've accidentally picked one either on the 'woods' tab or on the 'unique choice' tab.
The exception is the carved-top Tele, which for some reason the builder always forces you to select a lam top and binding to cover the edges of the laminate, even though the body description page says it can be made from a single solid blank. (And I've got one which I stripped the finish off of and indeed, there's no laminate top on it, nor binding for that matter, so they absolutely can and do make them without lam tops.) In cases like that the best thing to do is e-mail Warmoth.
The jack hole size is entirely personal preference. There is no functional difference, it's just a question of what kind of appearance you want and which jacks/jack plates you have easy access to purchase. The Warmoth site details how all the different jacks look and Warmoth keeps all the standard jacks and plates in stock. If you want a 1/2 jack hole, order a 1/2 jack. If you want a 7/8, order a 7/8. There's no better or worse, it's entirely personal preference.