Built In Bookcases

I'm not a woodworker, but if it were my house and they were intended to be in a permanent location, I would want the base molding removed so they sat flush to the wall. And I'd save the removed moldings "just in case."

When I built the bookshelves in our den some 30 years ago, I removed the base trim, installed the bookshelves, and then reused the base trim around the base of the shelf units. (Sorry for the run-on sentence).

Might depend on preference of the client.  If rental property, leave base molding.  If client wants to be able to take with them when they move leave base molding.

If leaving base molding, could always make trim molding for sides and top covering the gap, scribed to base molding.

Second option is to notch the bottom to lap over the baseboard.  Third option is to put the shelf units on toe-kick boxes as described in the kitchen cab thread.  Either way, the shelves will be flush to the wall and the h-o won't have to hassle with replacing the baseboard in case they move.

This.
" Second option is to notch the bottom to lap over the baseboard."

I'd take out the base board trim as the best option to offer to the client.  However, if floor/walls aren't true then you still might have to do some base building or shiming and covering up that.  You might have to scribe the cabinet to the uneven walls too....might want to plan for a filler piece if walls are uneven on the side of the cabinets.  I had to do that for our butlers cabinet.

I did quite a few of those 30 plus years ago.  Many were around a built up next to a fireplace surround.  I always removed the baseboards and trim so I could get flush to the surround or the adjoining wall.  If it didn't have a toe kick then I would reuse the trim.  If the bookcase went all the way to the ceiling I would use a separate base, usually with a toe kick.