* It's possible to implement custom security protections at a lower level than accepting whatever is provided by a microcontroller or implementing it in more vulnerable software.
* Many microcontrollers can be copied easily, but FPGAs are often used to run sensitive bitstream that contains proprietary hardware/software, manufacturers generally provide better security protections, such as verification and encryption, against data extraction (read: OpenPGP private key) and manipulation attacks.
* Most "secure" microcontrollers are guarded under heavy NDAs, while they are commercially available (and widely used in DRM systems), but it's essentially useless for the FOSS community. On the other hand, because the extensive use of FPGA in commercial systems, security is NDA-free for many FPGAs. It's often the best (or the only option) that provides the maximum transparency - not everything can be audited, sure, but the other option is using a "secure" blackbox ASIC, which is a total blackbox.
Unfortunately, nothing is foolproof, manufacturers leave secret debug interfaces, cryptographic implementations have vulnerabilities, etc. Hardware security is a hard problem - 100% security and independent verification is impossible, making it harder to attack is the objective, but it's worse than software - once a bug is discovered and published, the cost of an attack immediately becomes 0, and it cannot be patched. We can only hope that the increased independent verification, like the researchers behind this paper, can somewhat reduce these problems systematically.