Yes, FS-UAE is based on the emulation code from WinUAE 2.5.1. This applies to FS-UAE 2.2 and the upcoming new FS-UAE 2.4.0 stable version.
Code from WinUAE 2.7.x is merged into the development branch of FS-UAE and will be relased in the upcoming FS-UAE 2.5.0dev released.
Edit: there's newer FS-UAE versions for Debian available here:
http://fs-uae.net/download-beta
