Some default settings in SWI are not ISO-compliant (for example, it uses a string type that does not exist in ISO). But these are minor things that won't usually trip you up when feeding it ISO code. You can set flags to get it to conform in the way you want. And you should set flags whenever you want your ISO Prolog programs to be portable, because the standard is very lax and leaves a lot of things implementation-defined. But it specifies the flags to get implementations into the state you want.
Some default settings in SWI are not ISO-compliant (for example, it uses a string type that does not exist in ISO). But these are minor things that won't usually trip you up when feeding it ISO code. You can set flags to get it to conform in the way you want. And you should set flags whenever you want your ISO Prolog programs to be portable, because the standard is very lax and leaves a lot of things implementation-defined. But it specifies the flags to get implementations into the state you want.