I've tested this with my current theme (child theme of Suffusion) and with TwentyTen.
With the Flattr plugin enabled, excerpts display with unlinked ... at the end, rather than either the default linked version, or my custom text which has been set in both themes.
I've seen a previous post relating to excerpt issues - not sure if this is a related problem.
http://wordpress.org/extend/plugins/flattr/
The fix suggested in this thread makes the problem go away.
I'll mark this as resolved, as this works for me.
The part of the code you mention was something that I took over from the former dev. I'll investigate further...
In the next update there is an option to choose wether you would let the flattr-plugin handle excerpts or wordpress. I wouldn't want to remove the option completely because I can't tell what it might break... (yet)