I ran into the same problem. One thing you can do though is make an "enclosed" garden by using the foundation as walls. When you make a 1st level floor, raise the foundation up to a comfortable setting and then use the sledgehammer tool to remove the floor. It will just leave the foundation walls which a sim can then walk down into using a stair setup. Everything else can be placed within the foundation walls as normal including fountains, plants, etc. They use this trick to make split level houses but your garden could work, be on ground level, but would be "walled." Good news is you'd have three levels of foundation to work with. Also, you may have to place the stairs when the flooring is still there and not after but if you use the smallest foundation setting, the stairs would be quite small.
A helpful hint: You can enlarge objects, plants included, by holding down the "shift" key and pressing the "]" and "[" keys to make the object larger and smaller. You can then place plants and landscaping around the foundation of the house in such a manner that it hides the foundation. If you choose the largest size foundation (about a standard wall), then you can create an effect that causes the house to appear as if it is sitting on a small knoll or hill.
This may work as a work around.