Thay are NOT design flaws. They are very creative mechanisms to
improve processor performance. Just because they can be exploited
by parties with malicious intent does not make them flaws.
A thief can very easily smash the windows on your car or home to
quicky gain entry. Does that make car windows or home windows
a design flaw?
No. The only flaw is the thief.
But such security concerns are hardly relevant to a desktop
workstation. Only public-facing servers that host virtual machines
need to cripple their processors.
Keep in mind that the security obsession goes well beyond things
like Meltdown or Rowhammer. I believe that most distros also
build all software with protection schemes like stack protection
and "canaries." Since GNU/Linux is mostly C programs the addition
of a canary to every subroutine call can be quite expensive.
Gentoo offers a hardening option, or profile, that users can select
to produce a hardened and protected system, but others can choose
to ignore it all.