I don't recall if you posted this before, and if so, what I said, but I have decided, based on the recent questions you have posted on vowel harmony, that "flutuação" here refers to 'alternation'.

So this is how I would handle it. (Also, keep in mind that ''contudo" means 'however'. This has come up a couple of times before, and it's important to the meaning of your sentence.)

"The tone on the unstressed root vowel in the lexicon is low; HOWEVER, the pitch may be elevated because of alternation with the unstressed syllable."

30,600 refs for ["vowel harmony"+alternation]:

n this usage, umlaut is a specific case of **vowel alternation** that has developed from a historical instance of **regressive vowel harmony**. ...
en.wikipedia.org/wiki/Apophony



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Note added at 8 days (2007-06-16 05:27:46 GMT)
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First, please excuse me - I won't try to put in diacritics because my computer locks up, . Ten of the definitions in the large Aurelio dictionary (Port=> Port) refer to a back-and-forth or alternating situation - e.g. "6. variacao alternada." The 11th definition, from physics, refers to a distancing from the average or most probable value. I think you should check with the author is using the term in the more common sense of variation or in the sense of departure from the norm.