I looked at the source to figure out what it did.

The Enigmail website documents it as follows (note: seahorse is the
gnome-keyring GUI):

https://www.enigmail.net/documentation/advanced.php

---
Use gpg-agent for passphrase handling: GnuPG version 2.0.x is distributed with 
the GnuPG passphrase agent, a tool for caching passphrases. This is especially 
useful if several passphrases are used. Enabling this option makes Enigmail use 
the gpg-agent also for GnuPG version 1.4.x (requires the tools gpg-agent and 
pinentry to be installed!). Note that in some distrubutions, Seahorse is 
installed instead of gpg-agent. This may cause trouble when using OpenPGP 
SmartCards. If you use a smartcard for your key, then either use gpg-agent and 
enable this option or unset it AND make sure the environment variable 
GPG_AGENT_INFO is unset prior to starting Enigmail since GnuPG expects 
gpg-agent be running once it detects GPG_AGENT_INFO.

Do not activate this option, if you want Enigmail to ask you for your 
passphrase.
---

If you want Enigmail to change the documentation to make the current
behaviour clearer, please file a bug on their website, and attach it to
this bug:

https://www.enigmail.net/support/bugs.php

Thanks!

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https://bugs.launchpad.net/bugs/1325832

Title:
  Enigmail uses GCR without user confirmation

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