The reason the implementation is named (Rakudo), is because there's a spec, and originally there were a few people making implementations. There was good effort from individuals on C and C# versions that were more monolithic, and Rakudo was where most the community work went since it was designed in a way to be more cross platform (it's mostly implemented in the minimal NQP languages, which is "not-quite perl". It's a much easier thing to port to a VM, and then you get like 90% of the language features already designed and working).
The reason the VM is noted is because it changed a couple of times. Bringing the VM name into it lets people know that if it's different, maybe it will have fixed their main performance complaints. To my knowledge, they haven't used parrot in a decade or so, and there's actually some bad blood between the VM and Perl 6/Rakudo (which had different teams, another reason to brand with both.
So, Perl 6 is the standard. There have been multiple implementations to varying degrees of completeness, including but not limited to Rakudo, Pugs, and Niecza. Those implementations have generally targeted one or more VM targets, including Parrot, MoarVM, Java, .Net and custom VMs.
It may or may not have hurt adoption seeing this terminology, but it was there for a reason, because it denoted very large important aspects of what was going on behind the scenes, and in some cases doing otherwise could have worked against some relationships that were going on between projects.