Pro and Indie have the same features, there's the income resctriction but that's it.
So, what are the 3.0 features you're missing in, say, 2.5.8? Let me guess: Utility, Mesh and Voxelizer modules. Those are included in the Indie and Pro Editions. So yes, you're asking for a free Indie/Pro upgrade.
You're the OP, you said you bought Qubicle during beta and couldn't buy "the commercial version". I'm not sure how could that apply to "supporting Qubicle", mostly because I've made efforts on my end to pay three times for different Qubicle versions. For what you say it seems you paid once (upon a time) and want the latest version for free. I may be mistaken but that's what it looks like. As clear as English is not your mother language; I can address you in several others if you want my points more clear, just let me know.
It's common practice to have minor version free updates (1.1, 1.2, 1.3...) and providing discounts for existing users when a major version is released (1.x, 2.x, 3.x...). That's what we got, with price ranges way below those of Autodesk or Adobe to name a couple. I could argue about setting up dates such as "bought before" because I feel those who purchased 2.X early are as valuable as customers as those who bought it later. I could even add that offering upgrade discounts to 1.x users would be nice. But free major version upgrades should be exceptional, not the norm.
We could talk about the need of a voxelizer while we're exporting objects with the same t-junctions and optimization issues from the first version. We could discuss about the "slicing" of Qubicle in DLCs, even about how Steam may help Qubicle, its creators and users. We could talk about a lot of things more interesting than "I own a previous version and want some freebies". And please, check again the prices; you said 40€ but I think in your case it's closer to 25.90€ (VAT included). Log in to the Update Center with your order number and email, hit buy, enter the code and then tell me.
Edited: Messed up versions line, it's better now.
Edit 2: Quoting Qubicle's Support Center
For a Qubicle 2.0 license ordered before November 29, 2015 you will get
Steam keys for Qubicle Voxel Editor and Qubicle Utility Module.
Does that work for you? Free Qubicle 3.0 + Utility Module?