Thanks for the sketch of the apron under the lip of the top. How would the leg come into this? Take a 1/3 width strip off the inside of the apron and 2/3 strip off a leg then push it on like that? The front of the apron should be flush with the leg shouldn’t it?
No, don't shave your legs. Seriously as others have pointed out, stout legs are what a bench should be about.
When you first mentioned aprons I though you were building a trad 'English' bench (a bit like Jacob's picture) , with aprons used to provide clamping surface for longer boards on edge in the vice and also provide a joinery solution (the dado which houses the outside face of the legs).
_If_ you're building one relying on the thickness of the top to house some chunky mortices to stiffen the whole structure (more like a French/Roubo bench - there folks, I've used the R word) then I'd question if you want aprons? My current bench is 3.5"+ thick with legs blind morticed into the top, no apron, the front edge of the of bench and legs are all coplanar and I have dog/holdfast holes as another poster has mentioned above. The apron sketch related to a previous trad bench I built.
I can't see from your pictures if the 3x2 top is 3" or 2" thick, 2" is probably too thin to work with no horizontal supports underneath (especially across the laminated grain and if you've got integrity issues with the joints) and might need a redesign to the more English/trad style with a cross rail. Also to echo someone above, through mortices probably have issues here due to wood movement
If you still need to use a design with aprons, keep the legs intact, set them into the inside face of the apron(s) 1/3 of the apron thickness and if you want a full coplanar front, built out the lower legs to the same level.
There are lot of resources on the the web/youtube and some good books, but to start with the free stuff try searching through
Paul Sellers/Woodworking MasterClasses - builds a workbench from construction timber, I think the full series is on Youtube. This is a Trad bench, not everyone agrees with Paul on everything ( me included) but this could be an instructive series
Chris Schwarz/Lost Art Press/Popular Woodworking - Google will return a number of videos on building a French/roubo-style bench. You may also find Trad/English or 'Nicholson' bench styles. ++ FREE someone also posted last week on this forum that Chris's latest workbench book was up on the web for free download. I haven't checked this myself but it's likely to be worthwhile.
Richard Maguire/The English Woodworker - has subscription video series building both a French and an English style workbench - pragmatic and hand-tool based. Some of this may be shared out there as teasers
And to your last point, flip the top, place the legs on it and use them to mark the mortices, it looks like you're already adding rails/stretchers to the base so use that assembly as the reference for those mortices, don't just try to measure.
Good luck