You have not posted any info suggesting a fertility problem. Low T can make sex difficult, not the same as a low sperm count. TRT will for almost all guys, shrink the testes and fertility then can be a problem. hCG will keep the testes in form, but then sperm counts can be lower as there is no FSH, although it is believed that hCG weakly stimulates FSH receptors. If you need to pop a baby and sperm counts are not sufficient, you can take nolvadex for a while, dropping hCG. Then LH and FSH will typically come on stream.
Some convert T–E2 strongly in there skin, less to get into circulation.
I do not know what the effect is on LH/FSH for hypothroidic non-absorbers. We do know that some of these have lower T when applying, suggesting that HPTA shutdown is happening. E2 could do that.
Androgel and other similar weak T products that need to be spread over a large area of skin have the highest T–>E2 rates, because the large area exposes a lot of aromatase in the skin to high concentrations of T. And when guys apply small volumes of 10-15% T creams to small skin areas that there the E2 levels are lower. We have seen that in guys making that switch. I injections avoid the high local T concentration effects in the skin. Note that AI drugs can have difficulty managing T–>E2 in the skin as the competitive drugs cannot compete with the local super concentrations of T.
Note that elevated E2 will increase SHBG and that lowers FT, and for some FT is a lot lower. And then the E2:FT ratio has become very adverse and with that estrogen dominance, some feel a much worse.