proper composting is more than just piling it up and letting it sit.
proper temperature needs to be achieved to neutralize most pathogens and weeds.
compost usually needs to be turned a time or two for best results and timing of the first turn is also important.
the pile should get to 142 degrees internally (yes use a deep thermometer, you can buy em at good garden stores) and then when the temperature begins to fall it should be turned.
it will then reheat.
chemical fertilizer does alter soil microbial activity. It does not stop it. The greater the soil organic matter and the wider the diversity and density of the macro and micro biota, the less the impact of synthetic fertilizer but also less need for synthetic fertilizer.
Multispecies cover crops on a garden plot also do wonders for building the soil. for best effect they need to be allowed to build sufficient biomass to put back into the soil. this means letting it grow tall before killing down or tilling down the cover.
if you have a good compost pile, or sufficient waste feed stock, composting is also a very good way to get rid of dead animals. We have a dairy farm that is running a trial on composting its mortalities now. So far they are very happy with the results.