You should not have issues with AMD and linux. In general, the latest AMD processors, particularly those with high core counts, perform better on linux than on Windows.
The booting issue with Ryzen 3000 was resolved long ago, fairly soon after launch, by a workaround to systemd and also BIOS updates. https://www.phoronix.com/scan.php?page=news_item&px=Ryzen-3K-RdRand-Systemd-Maybe
What is more disturbing is that the root RDRAND issue is/was a long-standing issue from many CPU generations ago: https://bugzilla.redhat.com/show_bug.cgi?id=1150286
The rougher experience on linux was with AMD APUs, which seems to have settled down, though I’m not sure if they’re fully resolved. The non-APUs have been much less troublesome.
I would not hesitate to get AMD, and I’ve been running a 2700X with Fedora since launch with no problems. However, which CPU you get should depend more on your workloads.
For example, Intel has the advantage of better AVX and library optimizations (Zen 2 finally has a real AVX 256 implementation) which gives an edge for certain numerical computation applications. Plus, Intel is much better when it comes to the software and optimization side.
AMD is better now in just about everything else. Overall performance in many/most applications, PCI-E lanes, ECC memory support, price/value, and excitement/novelty factor, plus not being vulnerable to as many of the hardware bugs which keep getting found and thus not suffering performance penalties due to their mitigation.
If you’re worried about hardware bugs… Intel should be the last option on your list
In the end, your CPU choice should ideally be guided by your use-case, but in general AMD + linux works just fine.