Is adding a supplementary credit transaction something that could improve online payment security?
Answering my own question to be able to flag it as answered and prevent it from popping up from time to time: this measure appears as a plain example of security theater.
Here are the elements leading me to this conclusion:
I asked their support teams then reason behind this change: while they were usually quick to answer more usual questions I never received any answer to this one.
The change was apparently clunky and not well thought: they had to add a special functionality to allow onetime and prepaid cards to bypass this measure a few weeks after enabling this system as, obviously, a section of their customers weren't able to proceed with the payment step anymore.
This process is exclusive to this website: this a good thing to impress their customers but, from a technical point-of-view, this does also mean that no one else ever wanted or felt the need of such a system. It never takes long for new and genuinely efficient security-related ideas to spread, under one form or another.
This process is directly noticeable by the end user, which is required for an effective security theater measure.
I never saw any advantage to this measure, neither did any of the other Security.SE contributors for the two last years.
If anyone has some knowledge which could change this conclusion, feel free to add your own answer, but after two years I think I can safely put this one in the security theater bin, alongside with other ideas resulting from "pseudo-security as a marketing argument", "you hired a too zealous security intern/company" and "we need to justify our budget".