There are several factors here...
One is the converters you are using..second is the machine you are using and third is indeed the audio engine within the application.

Pro Tools by history has always had their own sound...very mid rangy and not too bright. Lack of stereo imaging as well. This has a great deal to do with their interfaces. The newer HD systems are not as bad as the Mix systems were but still lacks some of the stereo imaging compared to better designed converters.

One thing to mention here is that it's more in the way that the mix is bounced down or exported. To be honest I never use the internal mixing/bounce down feature of any audio application. I do my mixes in the system then record them in real time to my laptop.

When you hit render/bounce down or export audio mixdown you truly do not know what is going on with the mathematical process. Even if you are listening to a real time bounce...don't trust what you can not see or hear basically.

I've AB'd mixes that were recorded externally vs internally mixed down and there is a huge difference!

Anyhue, back to the question at hand here...yes, each application has their own sound and you will get everyone saying that their application sounds better.

From my experience, I've listened to most of these apps and I have to say Samplitude actually sounds really nice..the drawback to that application is that it's rather confusing to use unless it's the first and only app you've used!

Cubase/Nuendo is right below it then Pro Tools.

Opus