Its not the amount that is the limit, its the score that is associated with the trophies that matters. Just like on Xbox, no retail game can have more than 1000 gamerscore unless DLC's add extra achievements (which I believe are capped at 200 possible points). Trophies work in the same regard. You can only have 1000 points of trophies in a PS3 or 4 game with one little twist. The platinum trophy that is awarded for completing all does not count in the 1000 point limitation.
So to your point, yes there can be an Xbox game with 99 achievements. Each of those achievement would only be worth 10 points, however. The trophy point system works like this:
Bronze - 15pts
Silver - 30pts
Gold - 90pts
Platinum - 180pts
So retail PS3-4 games can offer you a total of 1180-1230 (The plat trophy can push the cap just a bit, but almost all games will not combine for more than 1230 without DLC) points towards your PSN trophy level. I am trying to find the link that confirms all of this (I read it before, but it was a very long time ago) but it is evading me. The scoring conversion rate above is sound though. Go ahead and assign those point values to any of your RETAIL games on your trophy list and they should equal the correct amount. Downloadable (non-retail) games don't work by the same rules, and normally don't have 1000 points worth of trophies.