msmtp vs msmtp-mta package, which one to choose?

The Arch Linux Wiki, a great resource in general for all Linux operating systems, explains that msmtp-mta merely creates an alias for sendmail. This means you will have broader support for programs that require a sendmail compatible system.

There is an existing question which discusses how to configure the mailing system of cron. However, again, I would just recommend the Arch Linux Wiki which explains that msmtp-mta will probably cause cron to Just Work.

The package description for msmtp-mta documents that it is a wrapper which will pull in msmtp as a dependency anyway.

This package provides the regular MTA program.

This is somewhat obscure, but apparently means sendmail and newaliases.

The package's file listing reveals exactly what it contains. As of right now (version 1.6.6-1) it contains the following files:

/usr/bin/newaliases
/usr/lib/sendmail
/usr/sbin/sendmail
/usr/share/doc/msmtp-mta/changelog.Debian.gz
/usr/share/doc/msmtp-mta/changelog.gz
/usr/share/doc/msmtp-mta/copyright
/usr/share/lintian/overrides/msmtp-mta
/usr/share/man/man1/newaliases.1.gz
/usr/share/man/man8/sendmail.8.gz

(In case you are unfamiliar with Debian packages, the stuff in /usr/share/doc/mssmtp-mta is just standard metadata for the package, and the /usr/share/lintian/overrides are specifics for the lintian package integrity checker, probably to say that it's okay for it to ship the same binaries as some other packages which also implement the legacy Sendmail command-line API.)

So in other words, if you require sendmail on your system, install the MTA package; otherwise the base package should suffice.