The IK systems don't interfere with PaintSkinWeigtsTool directly. The locked joints, however, might make harder to paint some tighter areas. Better than disable IKs is to add some basic motion keys from bindpose to whatever relevant poses that open problematic spots, so you can see how the mesh deform by simply scrubbing the timelin,e while PSWT active.
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Maya2019.1 @ Windows10 & GeForce GTX1080Ti
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