Tim's comments are very useful.

I am also wrestling with both ELT and transponder antenna installation
issues and wonder why manufacturers don't install them, at least as an
option.

I have one of the ground-plane-less rubber duckies for my ELT and am
going to replace it with an internal dipole, mainly because its
location next to the canopy rear sticks it in my right ear! It will
work perfectly well inside the fiberglass fuselage, where it is also
less likely to suffer damage. I will probably do the same with my
transponder antenna also, although I may stick that in the nose above
my feet.

Certification of avionics is mainly to ensure that the signal is in the
correct frequency and transmitted power with unwanted signals below
stated thresholds. Transponders also need to be tested for encoding.

Antennas are less of an issue since almost anything of about the right
length will work and most transmitter stages can handle pretty awful
impedance mismatches.