But honestly, that is the point of having those ports on a computer. If you need them, they are just there. Someone with an old camera gives you an SD-card to copy pictures. It might only happen 1-2 times a year, but if you don't have it its annoying. and the SD slot is so slim, I don't think that space constraints it. Same with 1-2 USB A ports. Rarely use it, but there are situations when you just get someone's USB drive to copy a couple of files.
Same with HDMI, if you need to give a talk somewhere and prefer to bring your computer, in 99% of the cases they at least have an HDMI cable.
I also very rarely use these ports. But it's a professional machine and I expect things to just work, so honestly at least an SD slot, single USB-A and HDMI port would be quite helpful. On the contrary, I think old Thunderbolt cables are quite rare and used in special circumstances, probably mostly at your desk, so a dongle is alright.