Currently, Elementary OS Freya contains 31-croscore-elementary.conf in /etc/fonts/conf.d (which by the way isn't symlinked from avail.d)
http://bazaar.launchpad.net/~elementary-design/elementaryos/elementary-fonts/view/head:/31-croscore-elementary.conf
This file handles the replacement for Microsoft Fonts (Times New Roman, Arial...).
That's ok, but the problem is even if you install Microsoft Fonts (with ttf-mscorefonts-installer for instance), the fonts are still replaced. This affects multiple programs like wps office or scratch editor.
Try it by changing scratch editor font in the interface settings to Times New Roman. Close and Reopen the settings, the selected font will be Tinos.
Is that a wanted behaviour? because it sure sounds like a bug for users.
Just encountered this after installing (and then reverting) some packages from the Freya PPA on a vanilla Ubuntu 14.04 install -- for whatever reason, that file didn't get removed along with the rest of the elementary/Pantheon packages (I'm assuming because /etc/fonts is normally generated from fc-cache and so apt wouldn't normally move files into or out of there directly) and was blocking me from using Microsoft Fonts until I went and deleted it afterwards. Definitely a bug if it's not handled gracefully by the package manager.