the problem is the test tube is likely way less accurate then the hole I told you how to make here
if you want it to fit really nice you would need to take the test tube and grind it on a diamond wheel on a rotary surface grinding machine. Might not be hard to do if you are working with the university and they have a machine/glass shop. If they help you, when you buy parts, buy extra and give it to them (i.e. extra test tube), often they like the weird artifacts they get to keep from jobs. It makes it more cool/thoughtful then a normal machine shop if they are doing scientific things. This job is likely going to make them think a little because its non standard, you probobly need to offer some intradepartment cooperation and resources. For some reason I don't think the chemistry department is going to have this machine, unless maybe they are making their own cuvettes (little extremely precise expensive piece of glass rectangle test tube for photospectroscopy machines).
Also, if you want to put a test tube into a thin metal box and align it, you need to glue on some bushings to help align the tube (fat precise washer you can buy on mcmaster that has a precise internal diameter), or you can make the waveguide wall thicker before you drill/ream it, so you don't need two steps. Otherwise the long test tube will try to align with 1mm thick waveguide body, rather then a 1cm thick bushing. (i.e. get yourself two 1cm thick chunks of brass, braze them on the tube, then drill it, but then you need a stiff drilling machine. If you buy and glue bushings, you can make your hole first then glue the bushing in place over a 10mm rod that you insert through the waveguide before hand, with a bit of grease on it, so the glue does not stick there. Be sure to take out the center when the glue is not completely cured because I had stuff get stuck despite applying vaseline). This will be the tricky magical not enough resources moment, to add bushings to the hole.
Likely it will be hard to align the two holes, you need a machine to do it right. ask them for help
Also, aircraft trick : if you are sure the waveguide is good, like rectangular, after you drill your top hole, you can glue a BIG tall bushing to the top with super glue, aligned over a 10mm pin, let it cure, then drill down from the top with a long drill bit to make your other hole. You can tesslate bushings, to make a properly centered but different diameter hole on the other side, so you can make both holes reamed, rather then drilling a nasty properly centered but crappy edge quality hole on the other side with a 10mm drill bit. It would mean you need to glue a bushing into a bushing after you glue a aligned bushing on. Then you take it apart with fire, you would need to make sure the two bushings fit together. But then you can do it with a hand drill pretty good. And you might need a long length drill bit if you are drilling a thin hole with a drill bit aligned by a bunch of bushings. so get a 10mm ID bushing, center and glue it over a 10mm hole with a 10mm pin, then glue a 5mm OD bushing inside of the 10mm bushing, then drill through with a 5mm drill, then do the other side like you did the first side. you can make all sorts of structures with the bushing to make it more stiff, like put a long one in there.