Yeah but the Commemorative reissues came well before Encore, thus less mould degradation.

In the past decade I can think of the following uses of the 1984 Seeker mould:
+ 2001: Reissue Starscream
+ 2001: black Starscream
+ 2001: ghost Starscream
+ 2001: Collectors Edition Skywarp
+ 2001: Collectors Edition Thundercracker
+ 2003: TFC Starscream
+ 2003: Commemorative Series Starscream
+ 2003: Sunstorm
+ 2007: Encore Starscream
+ 2008: Encore Skywarp
+ 2008: Encore Thundercracker
+ 2009: reissue Sunstorm
So that's at least 12 different uses of the 1984 Seeker mould that I can think of. And if Takara used the same "core body" mould for the CE Dirge, CE Ramjet, CE Thrust and CS Dirge, that'd bring the mould count up to 16. So that's 8 uses before Encore Starscream and 9-10 uses before Encore Skywarp & Thundercracker.

With that many possible reuses of the Seeker mould, it's not surprising that there would be some level of mould degradation - and obviously the more recent reissues of that mould would be more degraded -- as you pointed out, Hasbro's CS Starscream & Takara's TFC Starscreams seem to be of better quality than the later reissued Encore Starscream.

Remember that Encore Devastator is at least the fourth main reuse of that mould. Previously we had:
1. 1985: Original G1 Constructicons
2. 1992: "New" G1 Constructicons
3. 1993: G2 Constructicons

And it's been 18 years since G2 Devastator. So it's not entirely surprising that there may be mould degradation issues. Should TakaraTOMY have done something to restore the mould degradation? Sure. I feel that this is something that pre-TOMY Takara would have done (we know that Takara did extensively repair/restore the 1993 G2 Optimus Prime mould when they first reissued Convoy in 2000); I just get the feeling that pre-TOMY Takara would have done something to address the mould issues with Bruticus and so on... and it would have been rather surprising in the old Takara days if something like missing Mixmaster heads or incorrect guns frequently got passed Takara's QC checks. But unfortunately TOMY doesn't seem to apply the same level scrutiny as Takara used to.