With respect AdHoc, the better 6000 series are pretty good for strength. In particular the 6082 and 6005 alloys in T6 condition. 6063 is a pretty standard commercial alloy widely used and in several different tempers. For dinghy masts generally 6082 is used, generally it is extruded, treated to T4 condition, any cuts and welds, rolling etc carried out and then re tempered to T6 condition.
Whilst I suspect 6063 is adequate for this application, hardening to T6 would significantly improve the tensile strength, approximately doubling it. Note that welding it will automatically change the condition to untempered. Might even be better having a 'softer' alloy (6036 over 6082)to gain in toughness against any work fracture or fatigue from the pulses of the motor. Still worth getting hardened to T6 in my opinion. You can 'feel' the difference if you drill it or work it with a file. Or if you really want to quantify it, try a beam loading test, which will prove beyond all doubt how much stiffer the treated alloy is. Even more fun, try a beam of 6063 against one in 6082 both in T6, there is quite a difference.....
I suspect the 6000 series was used, as much more widely available than the 5000 series alloys. Certainly most non ferous stockholders here in the UK do not have off the shelf stocks of 5000 series box sections. Agreed, fatigue strength is a bit lower in the 6000 series but not usually too much of a problem for this type of application, a workboat used all the time would be different.