I doubt it has to do with the version of the motherboard. What makes you think that?
Can you check the following BIOS settings, if available, see if they are set properly:
Under Settings\Advanced\Windows OS Configuration -> Set Win 8.1/10 WHQL Support to [Enabled], Win7 to [Disabled]
Under Settings\Advanced\Integrated Peripherals, set SATA mode to [AHCI]
Under Settings\Boot, any Fast Boot options to [Disabled]
Under Settings\Boot\"Boot Mode Select", set [UEFI]
Under Advanced\PCIe Subsystem, set Above 4G to [Enabled]
Generally, these compact pre-built PCs are quite bad for future upgrading.
The problem is the same as in this thread:
https://forum-en.msi.com/index.php?threads/gpu-upgrade-for-trident-3-8th.396296/
Don't be misguided by the last reply of that thread, the amount of RAM has no influence on a 4060 working in this PC or not. It might depend on the model of the 4060 somehow. It would be good if you could take the PC to a local PC shop and ask if you could test one or two different 4060 models, and offer to buy it there if one of them works in your PC.
I would not replace the motherboard for this pre-built PC. I would keep it as it is, and save the money for later, to build a more modern system altogether. If you want to upgrade a system later, make sure to either build the PC yourself, or if you get a pre-built PC, i would make sure that it uses standard parts, at least a µATX-sized case (or full ATX size), normal ATX-sized PSU, and so on. With those small form factor pre-built PCs like yours, they don't use standard-sized parts for some of them, and later you have trouble upgrading.
