Charging for formatting with CAT tool work

Last year I had the displeasure of translating a file with particularly heavy formatting. Not only was it loaded with colored text, bold and italic type, it also had a lot of hidden text notes that were not to be translated. It was so bad that it inspired me to write a short guide on how to prepare MS Word and RTF files with content to exclude for translation in Trados or DVX. However, it also got me thinking that I really ought to find a reasonable way to start charging for the extra trouble of all these formatting tags. Clients have advantages from their inclusion in a job, but translators have extra work because of them, and this extra work should be compensated.

One possibility might be to take the count of inline tags (or codes as DVX calls them) and count each as the equivalent of half a word in addition to the usual measured word count. This would represent a fair level of compensation for correctly placing tags for cross-references, character formatting, etc. in a target sentence. It is also simpler and makes more sense than other ideas I was considering which involved statistical measurements of translation time differences as correlated to tag density in a text. Any other ideas? Objections to charging for real effort?