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When using a standard L bracket, the height of the lens does change slightly when you change orientations, but it is very rare that the change will make any difference in the framing of the shot. I almost always re frame after changing orientations with an L bracket, but that is normally because of other aspects of the shot, and not the slight vertical shift of the lens location.
If you use a bottom only camera plate and use a side slot in the ball head to "tip over the side", several issues have been mentioned above. One issue is that putting the camera body and lens off center from the tripod makes the support less stable for a variety of mechanical reasons. Another issue mentioned above was about the camera or the quick release clamp hitting parts of the ball head or tripod structure when tipped in to the slot, preventing full 90 degree tip.
The following are more issues that have not been mentioned, or that I want to again also mention. For the side tip in to the slot you are limited to around 90 degrees of tip maximum, so you can not go past 90 without flopping the whole setup around to the other side of the ball head. And a flop to the right side means that the hand grip would be on the bottom, which is useless for me. And the point above about needing the tripod pretty close to level in order to do a 90 degree tip and get a level horizon is a good one, and relates to the 90 degree typical tip limit. With a L bracket you can of course tip directly to either side quite a ways with no need to think about a slot. The next issue I want to mention is that in order to tip over the side, you need to loosen the pan base and move the slot to about where you need it, usually on the left side, before you can tip in to it, and that takes some looking and planning. And a related aspect of where the side slot needs to be located was the biggest issue for me, which is that to adjust the aim of the camera, including from side to side, you need to loosen both the pan base lock knob and the ball head lock knob to do your aiming, and then tighten each again to lock. With a L bracket, only your main ball lock knob needs to be manipulated. I often re-frame and shoot a variety of compositions for the same general scene, and having to play with both knobs, often on different sides of the ball head, was very frustrating to me. A final issue is if you want to do a panorama using the ball head pan base, a side tipped camera puts the lens a ways off to the side of the center of rotation, which may cause a different parallax kind of issue for some scenes.
I know I always get a good L bracket for every new body I acquire, and it spends a lot of time installed and used, unless I am not using a tripod and also care about the weight of the gear. So I highly recommend L brackets, and also very much like to combine them with a nice lever quick release clamp on the ball head to make a fast and easy to use aiming system.