There are ways around that, as far as Ruka goes. Gun barrels are "rifled" (have spirals carved into the barrel that causes the bullet to spin on the way out). Those spirals cut into the sides of the bullet while it's fired; ballistics compares the etchings on two separate bullets to determine if they were fired from the same gun.
The trick is: Fire a bullet from a gun into a large bucket of water. Return the gun. Put the bullet into a new cartridge. Fire the bullet from a smoothbore (no riflings) gun. The smoothbore won't add more rifling marks, so it looks like it was only fired from the first gun. (Smoothbores are much less accurate, so Ruka would have been shot at close range. I don't think this method could be used to have a second gunman shoot Akaza.)
Alternately, if Yukimura is guilty, he could have falsified evidence in various ways (swap guns afterwards).
I partly agree with you; both times we see Ruka getting "shot", there's no blood seen on her, and the powder burns on the curtain suggest she was shot from there.
The obvious series of events is: - Prop gun was replaced with live gun sometime between the end of rehearsals and when Souta took his gun. -- Killer lacks an alibi for some part of that interval.
My previous theory, under my then understanding of page 18, was: - Souta still had the prop gun at the time Ruka was "shot" - she was still okay - killer shot her at close range with the real gun - killer somehow exchanged guns - Souta shoots Akaza with the real gun -- Killer lacks an alibi between when Ruka and Akaza are shot, but could have a solid alibi up in the interval mentioned above.
Under your hypothesis, what would the killer gain from the scheme?
Also...
Seiya, Okajun, and Harumi have alibis for the key interval in the obvious series, so if there was any trickery, they're most suspicious. Seiya couldn't have known in advance that Itsuki would want to interview him, but the interview that gave Okajun and Harumi their alibis is obviously fake, so I think those two are most suspicious.