Your logic is flawed
1. Byakugan cannot tell the difference between Shadow Clones, rematch Naruto vs Neji noob, not to mention the fact that it was invented by the Second Hokage, who lived GENERATIONS after kaguyas death, she doesn't even know of its existence, just that there are obviously clones of Naruto.
2. It has been already stated that the only way to damage Juubi Jinchurikis is Taijutsu and Sage techniques. SO why are you *****ing that Sakura got a hit in, is it just because her name is Saukra? Did you miss Gai vs Madara?, noob (Also she doesn't blast out chakra from her fist, its like Gons Janken just more focused. Its all in her fist and it is just added to her physical strength. So according to your Logic Tsunade should never have landed a hit on Madara or his Susanoo. XD
3. She didn't use the blast attack because she's focusing on a Giant TBB atm. Never in Naruto history have i seen someone without a Clone perform 2 separate Powerful jutsus that require intense focus performed simultaneously. Not to mention she didn't notice Sakura above her. Bones and small dimensions are one thing, blowing yourself up next to a bijuu bomb is mentally retarded.
About your first point, you're talking about
shadow clones. Shadow clones are copies of your own self, so the chakra signature in each clone is the same, and hence Neji was trolled. That's not the same as a transformation jutsu, with which you pretend you're someone else. A transformation jutsu merely masks your outward appearance, but it can't change your actual inner chakra.
Your second point kind of discounts the fact that Kaguya's had her byakugan on, and byakugan users can't be snuck up on. She should have seen Sakura coming, although, yeah, she was distracted by Naruto/Sasuke/Kakashi. Still, Kaguya could have just teleported to another dimension again, like the Super Gravity or the Ice world. Even if Sasuke has amaterasu, it would have bought her just enough time to not be sealed. She just didn't do it because plot.
Third point, she should have made some clones then. Why is it that the only offensive moves this ***** knew were chakra punching, bone-throwing, and hair whipping? The final villain had three moves? Unacceptable, she obviously understood jutsus and how they worked judging by her analyses, so she should have been able to copy shadow clone from Naruto with her cracked out Sharingan.