Most people don't realise that there's a huge complex certification process that mobile phones have to undergo including the Federal Communications Commission (FCC) in the US, CE in Europe, and the Mobile Networks Operators (MNOs)/carriers etc.
Building a modular phone is all very well, but the phone as a WHOLE has to be certified. Mobile networks don't like users being able to change bits, they certify that a phone's compatible with their network and that's it, change something and the phone needs to be re-certified.
There's an opinion out there that operating systems are open source, and a lot of it is. The guts of it that talks GSM or GPRS or 3G isn't, in fact it's highly encumbered. Networks REALLY don't want you to mess with those bits as you can do nasty things to the network (in the good old days of TACS/ETACS you could REPROGRAM the network and set transmitter power levels etc.). That's why networks liked nice phones where you could only do certain things through the APIs and SDKs, there was no concept of 'root' and root couldn't play with those bits of code that operators didn't want you to mess with.
Google can afford the whole process, add a new module, certify the whole thing, it works. It all falls down when they allow 3rd parties to change things. The certification isn't for the module it's for the whole phone. Maybe Google have the clout to change the certification process, but as it stands it's not going to be easy to get carrier approval let alone regulator approval.
It's all well and good producing a modular phone, but is it going to work on real networks? Take your Ara with your custom modules, yes it may work (on a public network, but it's probably illegal), you might get away with it at Burning Man.
Yes Google 'could' certify every variation of the Ara that comes out, but it's unlikely.
Maybe the regulations need to change, but that's going to be a lengthy process and very expensive (well Google can sort out the second bit).
So though Ara may be the future of mobile phones, it's not going to be mainstream for a while and 3rd party modules even longer.