What element modifications are incorporated by the LEGOLAND builders?
The glue is one obvious thing, and I think they recently also experimented with a new sort of transparent stuff to paint the finished models with so that they would be more resistant to direct sunlight. I don't think they'll paint bricks to change their colour, though.

However, In the same category of things any respectable AFOL would never do, I'm fairly confident they'll also resort to cutting elements if needed. I'm unsure if that happens often and it's probably limited to parts where the cut isn't visible from the public. Another thing is the use of generic plastic sheets for some large windows, for which no LEGO elements exist.

Then, as Kramii said, electrical and mechanical components are never LEGO. For the vehicles, they do have a generic frame (metallic, with motor, battery, and all control electronic) on top of which they build a LEGO exterior. Presumably, trains follow the same logic.

So yes, they are very lax with what they can or cannot do. I know the work area of the designer in Windsor is visible from the public, not sure it is so with other parks (I don't remember that in the two others I've seen); but if you get the chance it's nice to see them. With some luck, they'll have some time to spare to chat with you.