One thing you should know, I just verified this to be sure : When the user picks "Fast Skin Shader" in the menu of the rendertree, it's always going to get and use the preset "SSS_Fast_Simple.Preset" in the factory install path. What matters is what is saved in that preset. Registrations, spdl content, etc.. it doesn't matter, it's what is in that SSS_Fast_Simple.Preset that makes what the default shader is going to be when you pick that menu item. Registration is especially meaningless, since everything is already registred and the number of parameters or location of spdl doesn't change. You shouldn't re-register factory things just for fun, this may break the setup software.
As previously written by matt, presets are not used when loading scene.
imho if there is any fixup you need to do on the render farm, OnLoad events are the way to go. Hard to write, but when you have one made, it's very useful in the future for various other things.
For getting the scenes right in the first place when they are created, you should have your own shader definition and material library.
However having a script that overwrites the factory presets with your own special variations would also be OK, if somewhat lazy. For example, a batch file to be used by users when they start XSI could get the latest version of presets from the network. I think this should be only necessary for shaders, which don't seem to look at other locations before factory.
Modifying/Replacing factory spdls, and especially re-registering softimage's spdls or shaders with modifications or other path is definitely *dangerous* and should NOT be doing that. This is pretty much a disaster waiting to happen, either now or in a future XSI update/qfe, etc. I just know something is going to go wrong later.
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