This can be a real bone of contention in any relationship - where does the step parents authority/responsibility begin and end. I know that it was difficult in my case having a very involved ex-husband (who ALWAYS knew better than either myself or my husband did about pretty much everything).
My husband and I struggled for years - arguing about how much authority show he have (he wanted more) and with the kids as to how much authority did step dad have (they wanted him to have none). We finally decided that for everyone involved, it would be best if my husband really had almost no say over any kind of punishment or decisions. If he was home with them, it was "wait until your mom gets home." If a decision needed to be made, it was "let's call your mom and see what she says." If I did need to hand out discipline, I always talked to the kids' dad first, rather than my husband.
It really was a sucky deal for my husband. He got none of the say, but all of the responsibility (he makes more than I do, carries the insurance, and has more sick days so often was the one who had to stay home with a sick kid to take them to a dr. appt. if their dad or I could not). Plus, with an ex who did not take his child support responsibility very seriously, my husband always had to pick up the slack.
I was pretty clear when we met many years ago, that although I am a "package deal" with kids and all, the package also included my ex-husband. He is their dad, he loves them just as much as I do, and he is entitled to make or be a part of every decision that is made for the kids. Period. 3rd wheels need not apply.
I can say from the other side where my ex-husband allowed HIS wife to be a large part of the kids' discipline process, it really sucked. She was not a very nice person and favored her own children over mine (which I can say would be tough for anyone not to do). Plus, in my opinion, she wasn't a very good parent - she lost one of her kids to foster care, and the other two were addicts. I always felt that she really wasn't qualified in many ways to "co-parent" our kids.
Fast forward to now - my husband has an EXCELLENT relationship with my girls. However, my ex-husband and his wife have little contact with them (mostly because the girls cannot get over how his wife treated them and that their dad allowed it).
If I were to hand out advice on this? If the dad is involved, then he has MORE rights than the step-parent. Not the same, not less. I can see like in your case, where the parent is absent, it would be a totally different story. However, for those who have a situation more like mine, it really would be "not your place".
Good question! I will be interested to see how others respond and if it is based on personal experience or observation.