Nope - there's a very basic difference. "Chip in" isn't transitive (no object), so "I would like to chip in that..." is incorrect, and sounds broken even if you don't think about grammar rules. "I would like to flag up that..." is possible because the phrasal verb is transitive (you need something to flag up), but it sounds a little awkward because you follow with a full statement. I've seen this phrasal verb only rarely - maybe other speakers in different places have seen it more often. Unfortunately, neither sentence sounds natural. If you think about the images behind "chip" and "flag", you'll see how different these phrasal verbs really are.