I recently moved a bunch of clips from one library to a newer one. Later on, while looking in my finder, I noticed that the original media files were still located in the older library and that something called "alias files" had been created for my newer library. I am currently in the process of creating proxy files for all the clips in my newer library...and I'm not sure if this is purely coincidence or not, but the clips with alias files -- clips that still have the original media files attached to my old library -- seem to transcode a whole lot more slowly than the newer clips (clips that were never in my older library and don't have alias files). Both libraries are located on the same external drive, by the way.
I don't think it should be significantly slower. It is actually using the same media files. What Finder reports as an "alias" is actually a symlink. There will be an additional single I/O per media file for the symlink but after that it should be cached.
Depending on hardware, source codec and proxy codec, there can be a performance difference in proxy generation. E.g, within the past nine months there was a bug fixed in FCP for Apple Silicon which previously caused generation of 50% H264 proxies to be quite slow.
Aside from that bug, proxy transcoding rate can vary considerably based on codec and hardware platform. On M1 Pro Apple Silicon and higher, generation of 50% ProRes proxies is usually very fast (esp. if source media is ProRes 422) because those have ProRes hardware acceleration.