This option is specific to transcriptome-only searches, a feature not yet implemented. However, transcript junctions can be used and the reported hits limited to those locations. Set "Use Own Junctions: Yes" to see the available options.
In Tophat/Tophat2, an alternate option that may be of interest is '-g/--max-multihits INT' and is named "Maximum number of mismatches that can appear in the anchor region of spliced alignment:" on the tool form. It can be found by setting: "TopHat settings to use: Full Parameter list".
We realize this is not the same operation. If there is an update about the implementation of this search option in the tool, we will update the post.
Best, Jen, Galaxy team