Acetyl is usually considered as a special case of an ether, and thinks like phosphates and sulphates as salts of alcohols.
kinase?s and phosphatase?s add and remove (or remove and add, I always get that mixed up) covalently bound phosphate groups from proteins. Those covalently bound groups are indeed functional groups.
Acetyl groups are not part of ethers, but rather, are part of esters. It just so happens that that the alcohol-derived component of the acetyl group is larger than the acid-derived component, and so gets nomenclature precedence, hence the need for something to call the smaller-two carbon bit.
Similarly, the non alkyl or non aromatic portion of a molecule may be bigger than the alkyl or aryl group, in which case the alkyl or aryl group is considered a functional group, eg N-methylmorpholine versus morpholine.
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