@Brian Krause's answer is completely correct. I'm only going to simplify it.
Tolerance to drugs develops because the enzymatic pathways (which are already in existence in the body, i.e. "are... endogenous homeostatic pathways") responsible for its metabolism enabling its removal from the body are increased, either by increased rate of metabolism or increased production of the enzyme(s) responsible for the drug's metabolism, etc. One of the most widely known such enzymatic pathways is the Cytochrome P450 pathway. (These are not the only ways tolerance develop, just the easier ways to measure.)
Tolerance to drugs is more noticeable because most drugs are xenobiotic, i.e. substances foreign to the body (or "exogenous substances"), so we must ingest them to get the intended effect, and the effect is noticeable, so when tolerance starts to develop, the dosage must be changed. So it's easy to observe tolerance to drugs. However, substances produced by the body are regulated without our being aware of it, because we're not visibly or otherwise noticeably actively doing anything; our bodies are to constantly compensating for internal processes, e.g. regulating our blood pH, glucose levels, etc. In a healthy individual, this is normal homeostatis, e.g. through positive and negative feedback, up- or down-regulation of substances produces, etc.. You mentioned hormones; thyroxine is a good example. Thyroxine is needed by nearly every cell in the body. The pituitary gland monitors (and controls) blood levels of thyroxine through the production of thyroid stimulating hormone (TSH) Low levels of thyroxine stimulate the production of TSH, whereas high levels causes decreased TSH production. of We're just unaware of all the regulation our body does until it overwhelms our ability to maintain homeostasis and becomes a problem of some sort, e.g. hyper/hypothyroidism, T2D (type 2 diabetes.), etc.
Cytochrome P450 Structure, Function and Clinical Significance: A Review
Physiology, Thyroid Stimulating Hormone