I used to design big combline filters, typically held together with 100+ M3 screws, and we'd make 25000 a year of a design. I know a few things about screwing
You can force a standard A4 grade stainless screw into aluminium, but unless you drill the hole at 2.75 instead of the 2.7mm that you'd use for a roll tap then there's a significant risk it will snap the screw. By significant I mean more than 1%, which doesn't sound much, but when you're putting in 2.5million screws a year us a lot of rework. And with the hole drilled at 2.75mm you lose a lot of strength, risking stripping the thread when you tighten it.
You can use trilobal threadforming screws, These are more expensive then normal screws but the snap rate is about 0.2%. That is low enough to not worry the hobbyist, but would still have left 5000 items of rework a year on a single product.
Unless you need the thread going to the bottom of the hole, then a single tap is fine. There only needs to be 3mm of good thread to hold an M3 screw, if you can drill deep enough so that the lead of the tap is beyond the depth of the screw then it's pointless faffing about with three separate taps.
The other useful trick we used was to counterbore each hole, just about 2.5mm diameter for 1mm depth, so that any burr raised when tapping or extracting the screw would sit in the counterbore and not hold the lid off the mating surface. We'd use custom form drills for this.