It seems like nobody here has done the waterjet in that thickness of aluminum. (Nor have I). I presume that your original post is a question to see if anyone else has had problems/pitfalls with this particular procedure for small holes in thick plate. I also presume that your question only arises because you don't really care how the holes get there, just that they get there, i.e., "Hi, Mr. Hole-Punching Contractor, here is my part, put holes in it please," and then you don't really care if it's some alien technology that puts the holes in there, as long as your part is returned perforated.
In that sense, I have never had any problems with using water jet and having extremely tight precision, but this particular case (small hole in thick plate) may require you to send a scrap piece and have them put a dozen holes in it with their process to verify quality. The only experience I have with water jet is that at the original penetration, (the bottom of the hole at the start of the cut), it is much wider than the kerf. Note that the bottom blowout is much smaller than 0.25", but that was also on thinner material. If they say it should be no problem, then it probably isn't a problem, but I would definitely get a sample piece done, in order to make sure that their salesman isn't making promises that can't be kept.
Engineering is not the science behind building. It is the science behind not building.
