First off, The Cambridge Grammar of the English Language does not recognize 'conjunction' as a part of speech. All items categorized under that heading by dictionaries are either subordinators, coordinators, or prepositions depending on their syntactic properties.
The two examples you gave do not have though and but serving the same function, and can illustrate some of the differences between the two.
[Though tall], he was not good at basketball. - concessive adjunct (PP)
He was [[intelligent] [but unkind]] - coordination in predicative
complement function with 2nd coordinate marked by but (AdjPs)
While maintaining the same meaning, Though could not be removed, whereas but can.
Tall, he was not good at basketball.
= He was not good at basketball because he was tall.
He was intelligent, unkind.
= no change in meaning
The adjunct headed by though could be moved around, whereas the coordinate marked by but cannot.
He was, though tall, not good at basketball.
He was not good at basketball, though tall.
*But unkind, he was intelligent.
*He was(,) but unkind, intelligent.
but acting as a coordinator cannot occur in initial position in a coordination, and the coordinate it marks cannot be moved out of the
coordination it is a part of,
though heads PPs that act as concessive adjuncts which can be moved.
There are other differences as well, for example that but cannot occur with another coordinator, but though can occur with one.
It was a feeble joke, and though Anna laughed, she felt the tears spring to her eyes without warning. (Departures; McCorkle, Jill; Atlantic 1991)
*It was a feeble joke, and but Anna laughed, she felt the tears spring to her eyes without warning.
For a full discussion of the properties of coordinators, prepositions, and the reasons why CGEL draws the lines where they do, it is essential to refer to the text itself (Ch. 15, §2.1).