Become ONE (with power tools). It's just a box. How pretty you finish/trim it after putting hole(s) where you want them is up to you.
It's basic sheetmetal and plastic work. There are some useful tools and techniques, like a jigsaw with a metal cutting blade (also works better for plastic than a rougher cut blade, just slower), and masking tape layers over the work surface to not mar it.
There are hole saws for fans, though the larger hole saws start to get expensive and most computer box fans benefit more from flow with a rounded corner square cutout.
You can lay down masking tape, use a ruler and make a grid to drill smaller holes, and countersink them if plastic to get rid of a fuzzy edge on the hole, or just cut slots and slap filter panels behind them, held on with neo magnets if it's a metal panel, and those magnets can come out of old HDDs if you can't wait on some ordered online.
You can make a hole and file it out to put USB3 ports in a plastic bezel, and epoxy them in if there's no other mechanical solution. I realize it seems like a lot of work but it is not that much time once you have the technique down.
Any case is a trade-off, but most can be improved to better suit the needs of the parts in it. I'd almost rather carve new holes in a case than have to scrounge up scrap material to plug up extra holes (sources of dust ingress) where I don't want any, nor do I want 3+ outward facing fans and 2+ times as many filter panels to clean if it's not a high heat gaming system.
You can fabricate 2.5" bays really easy with sheet aluminum. You can put taller legs on so a bottom facing PSU doesn't suck your tea up through it.

You can remove the front bezel entirely and just slap a filter panel on with a painted metal u-channel frame around it.
Make your case exactly the way you want it then you aren't looking to buy any more cases, except one more so you have one to put a new build in while you keep using the one it replaces.