Combining == into one single ligature creates confusion. It requires extra care to distinguish between == and =. Better to leave == as it is.
I have zero problems discerning between '=' and the '==' ligature One is long, one is short.
May I suggest that if you are having difficulty distinguishing between absolute characters and their ligatures, to not enable ligatures at all, or simply use a different font? The point of this font is to provide ligatures, such as the one you mention. Disabling it is easy: use Courier New.
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I have zero problems discerning between '=' and the '==' ligature One is long, one is short.