Of course they are different. And appropriately called different things. Not RSM version1. Version 2 blah blah. I know they are different. When it's called that I think CM or raikage lightening amplification. Where they are just upping the output.
The RSM version 1, version 2, etc... that the OP is talking about however, is not just upping the output like the raikage's lightning armor. The different "versions" actually give Naruto different abilities (that are actually significant as well).
Version 3 gave Naruto access to truth seeking balls, something that base RSM and version 2 (Kurama's chakara only) did not. Versions 2 and 3 also allow Naruto to go into bijuu mode and use chakara arms and what not (something that base RSM Naruto can not do).
You are talking as if the OP is wrong in distinguishing between the different forms with different nomenclature, but if you analyze the abilities of each, then you can clearly see that they are at least worthy of distinguishing from one another.
Besides, what do you want us to call the modes? By your logic, then every time we want to refer to Naruto's strongest mode, we have to say:
"Naruto went into RSM + all bijuus' chakaras" or "RSM + truth seeking balls and cloak". Either way that is a mouthful to say and too tedious to type every single time.
Therefore version 1, version 2, and version 3 are appropriate ways to distinguish it.
You could also say something like:
base RSM
Kurama RSM
9 bijuus' RSM
Either way, some distinguishing in the nomenclature is necessary in discussion if people are going to be nitpicky with the whole thing about the form we saw in the war not being what RSM actually is.