When there is a set of parameters for drug-likeness such as MW, LogP, HBD, HBA, etc., why are some commercially available drugs which are known to best don't satisfy it?
Because Lipinski role is only high level filter for selection of hits. Even if some drugs not meet requirements of that role still can be used as a regular medicines because for example modern formulation which helps change PK etc.
Lipinski’s “rule” of five is a retrospective analysis of what properties will maximize the chance(not dictate) of a drug being orally bioavailable. However, most TB drugs and antibacterials in general do not follow the rule.
This rule is only for oral drugs. In general, any drug that is not taken orally does not need to conform to the rule of 5. In case of oral drugs, the rule is applicable as most drugs pass through biological membranes by passive diffusion. However, if a drug is a ligand (or is ligand-like) that is actively transported through membranes by transport proteins the compound may not obey the rule of 5.