The TC world refers to the front to rear balance point of the TC as the Center of gravity (CG).
The higher the floor level, typically the more top heavy the TC. The higher the floor level, typically the greater the winds effect on the TC, especially side winds. From what I have observed, a North to South bed typically requires a raised floor. Typically, an East to West bed is a non-basement.
To my knowledge, TCs with slides must have a basement to allow the slide to go out. Usually puts the floor at bed rail height, some may be at wheel well height.
To accommodate larger water tanks, holding tanks, and/or a North/South bed, a basement is usually required. I believe approximately wheel well height is the most common.
Although it is true smaller units the TC floor sits on the truck bed, it is also true of larger TCs, especially older large TCs. To my knowledge, none have slides, and usually have smaller water and holding tanks than basement TCs. My TC is a 11.5 foot TC, definitely not small. It is a non-basement TC, and sits flat on the floor. It is carried on my 2WD truck, and from ground to highest point is 10'3". On the same truck, a basement model would be at least 12-inches to 24-inches taller.
The downsides to a TC with the floor above the bed rails depend on your camping style and preferences. In my opinion, the taller the TC the greater the need for a dually, for stability. Not a must, but more stable. The higher the TC,the greater the wind will affect driveability, especially side winds. The higher the floor from the ground, the taller the step required to get in the TC. The taller the TC, the more attentive you must be to avoid Tree limbs. In my opinion, the basement TCs are more vulnerable to water line and tank freezing than non-basement TCs.
Wayne