This argument is seemingly somewhat undermined by the great variety of ships used by the Federation already. But the real differences and commonalities would probably be found at deeper levels: ships using a specific common type of isolinear chip would be serviceable, while ships that look much the same but have a different type of chip or rod or helix or bulb or whatnot would have to be phased out.
As for the types of commonality that today are of the most concern to, say, NATO, the bold new world of the 24th century would probably make most of them non-issues. Common ways of transmitting data would be a matter of pressing a few buttons that make the software rewrite itself; the hardware would already be flexible enough to cater for everything. Common "ordnance" for energy weapons would simply mean, well, pressing a few buttons that make the software rewrite itself, too. Most spares could be replicated, physical ammo likewise. Connectors and adapters for most things would be virtual or wireless - we basically never see plugs and sockets in Star Trek anyway.
The greatest incompatibilities might well emerge from cultural differences after all...