Q:

In a string of comments, including junk, should I flag the individual comments, or leave a custom flag on the post?

A moderator on GL made a meta post about flagging comments. The part of it I'm questioning is:

If there are more than one comments that should be removed, don't flag them individually because that can make it difficult to see what's what. When viewing a post, moderators see an overlay with the flags on that post. If there are multiple flags, the overlay can obscure the post itself. Instead, flag the post and leave a custom message explaining which comments can be removed and why.

That seems very inconvenient for the flagger, especially if there are a lot of comments.  If the above is only personal preference, shouldn't it be marked as such, rather than as part of the guideline in the post? 

A:

You should leave a custom flag and ask the moderator to purge all the comments. If any comments have value and should be retained, you can mention them specifically, so that moderators can undelete those specific comments after purging the entire comment thread.
From the guide to moderating comments:

if most or all of an entire comment thread needs to go, just flag the post itself and suggest that it be purged.

Moderators have the option to purge all the comments and selectively undelete specific ones as mentioned here:

If many problematic comments are interspersed with a few useful ones, purge the lot and then selectively undelete those that have lasting value.

In such situations, I generally use this custom comment: "Please purge all the comments in this post except comment #4".

If the above is only personal preference, shouldn't it be marked as such, rather than as part of the guideline in the post?

It isn't a personal preference, it is the recommended way as per the guide to moderating comments for flaggers

