short version: since this question received no answers in about a year, it is safe to assume, that the answer is: no, the eclipse find bugs plugin 2.0.3 (or earlier) is not capable of the workspace-level configuration of the mentioned options.
upgrade to 3.x.x or higher versions of the plugin. (i already mentioned that in the question above.)
if upgrading is not an option, you have to bulk update your .project files. now i'm pretty sure there's an xml tool or a nice scripting language, that is designed for this kind of problem (bulk update of xml content). but since i already had to solve this exact problem with a simple java program, i might as well recommend just that.
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