Well in the case of BT (bacillus thurigensis) cotton and corn, for example, the GM plant produces the Cry toxin which is bad for the insects that eat the crop, so better than spraying it (Also BT is used in organic agriculture via spraying btw).

Herbicides like roundup affect a certain pathway in plants, not humans in animals.

"And pesticides are bad for people and animals in the longer term too."

Not at the concentrations that are used. The amount of residue is minuscule and modern pesticides have far less toxicity than older ones that have been phased out.

IIRC, the BT toxin only affects insects that have an alkaline digestive system. Animals and humans are unaffected as its acidic.