I have not found any articles describing how the computers were selected. Mildly surprising because one thing Hollywood loves to talk about is how to get someone else to pay for making a movie.
Apple provided a translucent prototype and a prerelease PowerPC laptop. If the prop guys did the Compaq mod, great job capturing the look of what a teen with unlimited time and a well stocked junk bin would try to put together. If it was Apple using a Compaq shell to test logic board design before springing for a new clamshell mold, then there is an interesting story.
One of the images I have seen shows the keyboard close up. It is not a solid plastic cover hiding the Apple original but there are 3 smaller plates concealing each group of function keys. In the picture, the smaller plates are pulling up from the surrounding shell. Having the ability to pop the covers off and gain access to the function keys is a bit more work than a prop designer would do but might make sense for an engineer testing the idea of function keyless laptop keyboards.