I expect the answer to come from the developers of the Adobe Hunspell Plugin.
The same problem is found in the Hungarian hyphenation. This issue is critical at least for Catalan and Hungarian, and it makes the Hunspell Plugin unusable for these languages.
The Proximity Dictionary for Catalan hyphenation has many problems, and the Hunspell would be a great (and customizable) solution.
Our third party hyphenation product, MindHyph, can handle this. It adds support for the Hunspell Hyphen library for CS3-CS5.5
In the intel·ligència example, it's not possible to truly represent the hyphenation behavior in the edit box since it depends on where the word breaks.
With this example we have 3 hyphen points. In the first break, we strip the · character, in the second two leave the symbol. Like so,
Here's a screen shot illustrating this in InDesign.