The order of the functional groups and the numbering are done separately. The order in the full name is alphabetical, the order of numbering the C atoms is defined by IUPAC. It's not the same as Cahn/Inglod/Prelog - this is generally for stereochemistry and isomers distinction. But in IUPAC's order halogens still have higher priority than alkyls.
As an illustration of how the two things are separate, you can consider
2-ethyl-1-iodocyclohexane.
The numbering of the C atoms stayed the same but the ethyl group went to the front of the name because it starts with an 'e' as opposed to 'i'.
And one more detail - the di-, tri- etc prefixes do not count for alphabetization purposes. Which means that
2-ethyl-1-diodocyclohexane would be the correct name.