If the welcome comments are distracting, they can be removed and probably even should. So go ahead and flag them. As a mod, these are particularly easy to deal with, too.
Thank you for having an eye open for these things.
For what it is worth here are some of the points that I consider when writing these comments. There is a nice script/ add-on/ extension, AutoReviewComments - Pro-forma comments for SE, that automatically informs you how long the user is a member and how much rep s/he already gained. Occasionally I check if the Informed badge was already given. I post these comments to users which I think are new to the system and might need some guidance. I have addressed that on meta before: Shouldn't we be a bit more welcoming to new askers/ posters?
With that in mind, I will post the comment also to users, that have an association bonus. While I think that most users coming from a different network know about the system, I also sometimes see, that they don't know how to use the site. But I decide that on a case by case basis. Since comments are expendable I don't feel any harm doing so. I also think there is not right or wrong usage for comments (ultimately they should all be deleted).
When you start flagging these comments, make sure that you flag for everything that can be cleaned up, if there are multiple things to address, use a custom flag on the post itself (It is much easier to purge the comments instead of deleting all the flags).