For me personally it's simply because they aren't companions. They are main characters (origin characters) that will eventually all be playable as the main protagonist. None of these characters are bit players.. they are all main protagonists jostling for position. I don't feel like this is my characters story or that my character is in any way cool or special because all the "companions" are cool and special. It makes me feel like I'm playing with someone elses perfect party and frankly I'm selfish and want to play with my perfect party.
a custom pc feels more like a passenger then the one driving the plot - ive played through ea a couple times and i always leave it with the feeling that if my pc never survived the ship crash the whole narrative/story would still have carried on without me, a custom pc just isnt unique - like, everyone has tadpoles lol