MySQL connector needs useLegacyAuth=1 to connect to older MySQL servers but cannot find where to add this option in the Tools > Settings > External Tools dialogue

What connector version do you use?
I tried 6.02 with old mySQL dbs without any hassle.
http://dev.mysql.com/downloads/connector/c/6.0.html

I was using 6.1.3 (64bit). I downloaded and downgraded to 6.0.2 (64bit) and all appears to work now. Thanks. Although you may want to try and figure out why a newer version of the MySQL C connector is a fail.

Perhaps, that is between server and client. Since neither is ours, I better leave reasoning up to them (mySQL).
But I can see a potential problem if you need to work with some new and some old servers from the same client.
You may want to ask them why don't they fall back to legacy auth automatially and do this by default.

I have a Wamp install that uses an even old pre 6.0.2 library and doesn't work with either of these two.

It's just one of those library juggling things we have to do when working with multiple servers in multiple envs. Alas, but thanks for the 6.0.2 solution, another note made in the SysAdmin book