Uncle's cloth:
The cloth is red with two holes (not made by bullets) in it.
The color red is also another nod to the "Uncle is Red" theory, since everyone back in 2010 was starting to call him Red or Uncle Harlow.
Those two holes are a nod to Red's parents, but not Nate Harlow's cloth, if it was, why Uncle would had a cloth so special to him dirty like that?
Like the Cougar Man easte egg or Donkey Lady, R* saw how popular some theories and glitches were in 2010.
Outfit:
Uncle's outfit is not red because of "Uncle is Red", but because he's the spiritual successor of a Red Dead Revolver character, Curly Shaw, he wears a lot of red and has similar features with Uncle (beard, nose, hat)
Plus, both characters help 2 times in their respective games before going (Uncle leaves the gang and Shaw dies)
Conclusion: R* made RDR2 Uncle a nod to his most popular theory.