Don,
Tom has the right idea. You can create context-level (product/library/project) OIRs and have a different versioning scheme referenced than is referenced at the org or site level. The OIR evaluation hierarchy is product/library/project, then organization, then site. What this means is that attributes defined at the product/library/project-level take precedence over what is specified at the org and then site level. The org and site level OIRs are evaluated only for attributes that are not set in the already evaluated OIR(s).
The product/library/project-level OIR would need to only contain the following in order to just change the versioning scheme (in this case for a WTPart, changing the versioning scheme to a custom file-based scheme called MYSERIES):
<AttributeValues objType="wt.part.WTPart">
<!-- set the version info to a generated version info -->
<AttrValue id="MBA|versionInfo" algorithm="com.ptc.core.foundation.vc.server.impl.VersionInfoGenerator">
<Arg>wt.series.HarvardSeries.MYSERIES</Arg>
</AttrValue>
</AttributeValues>