Being the biggest star in the sport you're going to have power in negotiation. This is to be expected. In terms of being able to pick gloves, I will agree that the Maidana situation was somewhat ridiculous (not that I think it made much difference, but it was ridiculous). Having said that, outside of one claim by Chop Chop, I've never seen any evidence of Mayweather picking any of his opponents gloves outside of the Maidana situation. Essentially every big puncher he has ever faced, minus Maidana, got to use the gloves they wanted to. Mayweather was famously unable to convince the commission to use 8 oz gloves for a JMW fight when he fought Cotto (yet they did it for some reason for the Mayweather/McGregor farce).
In terms of judging, outside of the Castillo fight which happened well before he became a star (even if he was the money fighter in that matchup), there hasn't been a fight that you can reasonably argue Floyd lost, and if anything it's been more typical to see poor scoring against Floyd than for him (the 114-114 card in the Canelo fight being a major example). You can argue that he is able to exert pressure to choose certain referees, but it's not like most referees that people complain about (Cortez against Hatton and Bayless against Maidana the second time) have reffed out of character for those fights.
Cortez wasn't going to allow Hatton to flagrantly foul (which the British refs who Hatton got his whole career did allow), but his reaction to Hatton's plan wasn't something that I liked (they didn't always need to be broken immediately). When Hatton stopped tying up Mayweather and then going to work (which isn't legal) and instead attempted to infight legally, Cortez let them go and Mayweather actually got the better of the infighting (something Hatton has acknowledged on several occasions). All in all, I didn't like the way Cortez reffed the fight, but that is the way Cortez always refs infighting, and Mayweather was always going to beat Hatton.
As for Bayless, I've never liked the way he refs (he never allows much to happen on the inside, especially when fighters try and engage on the inside by first tying their opponent up), but he reffed the second Maidana fight the way he typically refs any fight. I think Floyd deserved a warning and perhaps even a deduction for frequently holding on the inside (initiating a clinch isn't actually illegal, but frequently holding on and not letting go once you get there is), but that's par for the course for Bayless. It's more a symptom of the way fights are refereed these days than anything else (and very few fighters can fight on the inside in this era, although, Floyd is actually one of them who can). At the same time, Maidana got away with a ridiculous amount in the first Mayweather fight without being penalized (not that I fault Maidana, that's how he had to fight, and that style is part of the reason I've always liked him). Even in the recent McGregor fight, the reffing was fairly poor in the sense that he didn't meaingfully warn McGregor for just about any of the flagrant fouling he engaged in (which, I'll say, included more holding on the inside than you'll see in essentially any Floyd fight).
All in all, bringing the kind of money to the table that Floyd does is going to give you leverage in negotiation and thus many small (and often trivial, but not always) advantages. Many other fighters have had similar privileges over a longer period of time than Floyd (Ray Robinson, for example, was even more controlling in negotiation than Mayweather), it's just the way boxing works. There isn't anyone else in the sport's history who has gone unbeaten fighting the type of opposition Floyd has (not saying he's the greatest of all time, or that it isn't easier in this era to control more things while fighting less frequently, just that it's still a remarkable achievement). t's hard to really point to any situation where any of these advantages were close to being decisive. For that reason, I think the fact that many people like to talk about all these things as if they really overshadow his achievements in any meaningful way to be a little ridiculous.