The decoupling was nice to have, but i've gathered that the bigger issue was 10base5 cabling was big and inflexible, and connecting to it was a bit of a chore, it was kind of necessary to have a flexible cable between the computer and the tap.

10base2 had a much more flexible cable, and allowed for T's, so it wasn't too bad to route it right to the computer, and 10baseT was also routed to the computer. So after 10base5 was pretty well dead, budget cards lost the transceiver port, although fiber transceivers were useful in niche cases -- if you needed one, you'd have to more carefully select your ethernet card.

Modern datacenter switches are still this way, see SFP+/QSFP.

Not just for that, though it's important--as I understand it, the electronics needed to feed data at high rates over RJ-45 are actually surprisingly difficult. Going much over 10Gbit (currently expensive) over RJ-45 is going to be prohibitive.