Ugh!
 
I do this all the time. It will probably be like 10 more years before I get used to switches for LEDs.
 
It does mean we need to pick a place for your switch still. Here's 2 options with the approved layout:

 
Please let me know if you like #1 or #2 for the LEDs, or if you want me to start over.

I was kind of hoping to see it slightly apart from all the other controls, like due east of the pickup selector in the picture above, but I wasn't considering that getting into the area where I tend to play more (neck pickup or in between the two).  If I had to go with one of the options you outlined, I'd go with #1.

I came up with another idea.  Swap the positions of the stereo/mono switch and the LED switch (option 1) and then move BOTH switches due west (toward the bottom of the bass when held upright) so that the stereo/mono switch is in line with the output jack.  Will that work?

Plotting it out on the bass:  

  I didn't consider that little dark spot so we tried this (green controls are moved slightly from the original layout):

 which covers 90% of the dot, unless you use the hat knobs, then all will be covered.  But then we need to move the switch to the small red dot or the 1/4" output to the large red dot to make them stack the way you want:

 Do you have a preference?

Nope.  Fire at will.

We keep finding new and creative ways to avoid drilling holes in your bass! Actually, we just probably overthink, but that's what makes us Alembic.   Ok, here's the layout done as I originally designed for this custom body shape:

 You can see the little dark mark, but it may or may not bug you.   Here's things rearranged slightly to concel that "beauty mark" under the skirt of the knob:

  Just wanted you to have a look at things with knobs in place before Swiss-cheese time. Let me know if you have a string preference one way or the other.

The mark doesn't really bug me, but option 2 bugs me slightly less, so let's go with that one.  Thanks.