Holder of a Palestinian refugee travel document issued by Syria - traveling to Amsterdam

I am not familiar with Dutch policies on this and I don't actually know if there is a (higher) chance they would send him back but I have some experience with other related situations.

For example, I know a number of countries that would let people holding a passport from Northern Cyprus enter their territory but still issue visas on a separate piece of paper and refuse to stamp their passport. The authorities of these countries do (sort of) recognize that passport in practice but make a point of officially demonstrating their lack of recognition of Northern Cyprus as an independent state by treating it differently than a regular passport.

Something similar could be going on here. Since he got an authorization from the Dutch authorities, I wouldn't be too concerned. It's possible that this is a separate document instead of a proper visa precisely to allow him to travel while still maintaining the appearance that his travel document is not officially recognized or something like that.

One thing you might want to check is whether the airline is familiar with the issue. I expect that a local airline would have seen such cases before but some other airlines might not. What you want to avoid is that your friend is denied boarding over concerns about the validity of this authorization.