Yes, they have removed the Confederate Flag and replaced it with a skull logo:
I think this is fairly embarrassing woke pandering, but somewhat predictable in current year. One thing I thought was interesting is that Kotaku reported this change as follows: "The remastered
Grand Theft Auto: Trilogy appears to be leaving the Confederate flag behind [...] the footage offers a brief glimpse of arms dealer Phil Cassidy, but this time without
the symbol of Southern slavery on his shirt."
This description has been lazily copied verbatim by games journalists all over the globe, yes I checked and it's literally been copy+pasted then translated on various gaming sites that cater to German, French and Spanish audiences respectively. To brazenly reduce the Confederate Flag to merely a symbol of Southern slavery is both ahistorical and laughable, but then again this is coming from the same people who believe the successful political retcon that the Civil War was about freeing the negroes in the South which is also an absolute fiction.
EDIT:
Seems a very strange decision in light of these comments:
Then again Dan Houser resigned from Rockstar in February 2020 and this point of view isn't shared by the new leadership.