Please reference ETC WIKI article in regards to painting S4 fixtures: http://www.etcconnect.com/community/wikis/products/knowledgebase-can-i-paint-my-source-fours.aspx
Please reference ETC WIKI article in regards to heat output of S4 fixtures:
In short, ETC recommends that you do not re-paint your fixtures but they are yours and you can do with them as you please. Others have tried various things to different levels of success. Try searching the ETC Forums with the search term 'paint': http://www.etcconnect.com/Community/forums/
Concerns over causing other damage: That is dependent on to how diligent you are in ensuring that paint does not get to areas that might cause your fixture problems. But as ETC does not recommend re-painting, we cannot really give you any guidance on the ramifications of re-painting.
In terms of ETC re-painting your units: I'm afraid that is not possible as all previous paint would need to be removed, the fixture taken fully apart, parts cleaned, and then repainted. The cost would far exceed the price of a new unit with 'custom' color painted on by ETC. (You can contact your dealer for pricing of S4 with custom color)