And you are wrong, again.with the exception of pc-only features and differences in ui, the 2.2.7 and console 2.2.7 are identical in-terms of mechanics, there are mentions of the refund mechanic on steam and reddit from the pc version 2.2.6
If it was a bug it was never fixed or even declared as a bug in future updates and by future updates i mean all the way up to 2.7.2 (the current pc version), in fact that particular upgrade mechanic that was introduced in 2.2.2 and tweaked in 2.2.6 never gets touched or changed after that point.
I've just checked 2.2.7 PC version (friend of mine likes to keep old GOG versions available), and bug is not reproducible there.
On PC in 2.2.7 it charges you the full amount to start upgrade, and refund is added only when each ship upgrade is completed. While on console it applies refund for initial upgrade cost and gives you refund one more time when ship upgrade is finished.
So it looks like a bug related to mixed code from different versions they've used to build release for Console.