How to hide/remove this foundation?

You can't adjust foundation for individual rooms. Any foundation height you apply, applies across the lot. You can remove a specific room (or flat, which is what it looks like you used at ground level there), but as you note, it will change the height of your columns, and you will lose your spandrels. Now what you may be able to do as a work around for the columns is find an object with a column like look to it, and use MOO to place it. It will likely extend up into your 2nd level deck, so it's a matter of whether you can make that work (by covering the spot with décor, etc.). Here's an example where I used the Wolf Pitts TruWood Lamp Essentials object as a column:

http://i916.photobucket.com/albums/ad5/SFsimpics/Sims4/Building/columnsworkaround_zpsu7xx8jkk.jpg