Sam,

No kidding.
I currently have a 4.0.5 M2 Client for testing, and active 4.0.3 and 3.0.1 Clients for productive work in up to four different environments The reasoning makes sense, though: if you remain downwards compatible (a higher version server can talk to a lower version client) you can schedule the server upgrade and then - team by team - upgrade the clients. If it was only the other way around teams who could not upgrade yet would spoil it for everybody else desperately waiting for new server features.
My guess is that ensuring both upward and downward compatibility would incur such an increase in costs that it would drive down the overall ability to bring new and desired feature into RTC.

So your choices come down to: use a 4.0.1 client to access both 4.0.4 and 4.0.1 servers, or use two different Eclipse Clients (on the same computer) to have one of them be version level 4.0.4

Normally I add a disclaimer to please mark the answer as accepted if this answers your question, but in this case I fully understand if you abstain. Still, the only answer I have.

Best,
Arne