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According to WWWJDIC and ALC, 耐性 is used for drug tolerance (e.g., 耐性現象), but 耐容 is used for radiation (e.g. 耐容線量). Based on that, my guess is that 耐性 can be used to express neutral effects like decrease in drug effectiveness, while 耐容 expresses limitations on harm.
Is this a strict distinction? Does the distinction exist at all?
The kanji 容 carries the meaning "to accept", "to allow". Similar constructs include 許容 容認 容赦 etc. The 容 here is used for the same meaning. I.e. 耐容 does imply how much it can tolerate harm being done. 耐性 on the other hand is neutral.
To recap, 耐性 can be used to refer resistance against both benefit and harm, while 許容 can only be used for resistance against harm:
Benefit: インスリン耐性 -> ok
Harm: 病原菌耐性 -> ok
Benefit: インスリン耐容 -> bad (unless you mean how much insulin one can take)
Harm: 耐容線量 -> ok
