Long Story Short, they don't work together. His ult deals exactly the damage it says it will, regardless of if they're at low life (aka, when he wants to be ulting). Same goes for the Havoc Mastery, though the effect is less pronounced.

I'm NOT saying he necessarily needs that bonus finishing damage, or that he should be going down the offense tree, but mechanically, it's a bit misleading... gives Darius NO incentive to go down that tree.

Define minor here then o.o
if ur saying that a 9/21/0 then deal pretty much the same damage as a 21/9/0 darius, except getting tankier and more CDR, then something is seriously screwed up mechanics wise

perhaps minor is a bit of an understatement, but it doesn't drastically change gameplay. It means, late game, you deal about 60 less damage on ult. Is it significant? Yes. Is it particularly game changing? Eh. Not really. But you are correct- 9/21/0 Darius is absolutely better as is

I thought true damage isn't supposed to be affected by them, just like they're unaffected by anything else?

People still go 21 offense on anything but mages?

Ha.

Executioner mastery ineffective on Darius' execution ability?

Dat irony....

you can't decrease true damage by any means, even % damage reduction, and last I checked, you couldn't amplify it by any means either.

Working as intended

this is working as intended. masteries do not increase true damage. olaf's reckless swing, for example, isn't affected by those masteries either.