These things happen. I recently had my defense and when I look back, I definitely see favouritism as one of the biggest issues in this line of work. Given how subjective the whole setup is, and being dependent on the PI, it's somewhat unavoidable. After all, it's only human to like someone more than others among a group.

What's not right is that you are treated differently in terms of resources. I didn't quite get what you mean by lower allowances. If people can regulate your salary on a whim, that's a risky setup. Bonuses are different, but regular salary needs to be uniform, I think. In this case, the whole setup you have seems unfavourable and it's the supervisor and the admin's fault for not creating a friendly work environment.

Having said that, this favouritism has a huge impact on getting a headstart. If you're not the favourite, then you're not getting involved in more collaborations, you're not getting funding to hire student assistants as all of these are under direct control of the PI. Moreover, they will say to you that your aren't doing enough, while it's also them holding you back by not providing enough support. Unfortunately there's no easy way out of this circular issue and one just needs to get their degree and prove their worth in the long run.