Hi there,
For example, if I create two new qubes, I use Whonix as a template and I also use Whonix as a network for both.
Can outsiders see that the two Qubes are still running on the same PC or can you generally see with temporary AppVM whether it is always the same PC on which AppVM is running?
If so, how can I get around this?
I would like it to be no longer apparent that it is the same PC. How can i do this?
Yes, Xen and VMWare hypervisor guests can be fingerprinted by examining TCP clock skews. Unique TCP-fingerprints of virtualized machines can assist in the remote detection of virtual honeynets. If the fingerprints are unique based on the hypervisor they run on , then an adversary could possibly develop exploits for the underlying hypervisor.
How can I prevent you from seeing that I always use the same pc?
Run a lot of vm, different template. and separate everything. 
@Tom0815 Computational Science derives causation, ultimately, from algorithmic correlation.
Hence, (unless you have a shielded computer which leaks no emissions), the answer to your first question is: Yes.
The answer to your second question is: there is no current mitigation (that I can tell you). Only avoidance: do not use Qubes if you do not want ‘outsiders’ to be-able to fingerprint you.
Unforunately, to the best of my knowledge* (if you believe me, that is), you cannot do this.
*See: (Tempest (codename) - Wikipedia)