Motivation: By separating the code which manages conversation with other Joinmarket participants from the code which manages this participant's Bitcoin wallet actions, we get a considerable gain at a minor cost of an additional layer: code dependencies for each part are much reduced, security requirements of the server/daemon layer are massively reduced (which can have several advantages such as it being more acceptable to distribute this layer as a binary), and client code can be written, implementing application-level logic (do join with coins X under condition X) using other Bitcoin libraries, or wallets, without knowing anything about Joinmarket's inter-participant protocol. An example is my work on the Joinmarket electrum plugin.
It also means that updates to the Bitcoin element of Joinmarket, such as P2SH and segwit, should have extremely minimal to no impact on the backend code, since the latter just implements communication of a set of formatted messages, and allows the client to decide on their validity beyond simply syntax.
Joinmarket's own messaging protocol is thus enforced only in the server/daemon.
The client and server currently communicate using twisted.protocol.amp, see AMP, and the specification of the communication between the client and server is isolated to this module. Currently the messaging layer of Joinmarket is IRC-only (but easily extensible, see here. The IRC layer is also implemented here using Twisted, reducing the complexity required with threading.
The "server" is just a daemon service that can be run as a separate process (see scripts/joinmarketd.py), or for convenience in the same process (the default for command line scripts).