Multisig is just one usage of p2sh and many many Bitcoin companies, exchanges and private people are using multisig addresses.
So when we take all the other services and private users into account that use multisig addresses the 97% of user funds Coinbase holds in multisig are likely far lower than 5% of all bitcoins, we can only guess.
The problem with your post is that you
are only guessing, just as you wrote. My
guess is that Coinbase does indeed own most of the Bitcoins in multi-sig addresses. I don't see why that couldn't be true. Multi-sig usage is very low.