MGM, I believe the reason for this apparent anomaly, as you rightly call it, lies in the fact that we are no longer comparing "pure" religions, i.e. based simply on the original tenets of each. Very quickly religions absorb cultural, ethnic, local etc characteristics. This happens either intentionally (dressing up an external belief or practice as "religious" in order to give it weight or to help subjugate others or to ratify a war or exclusion or a pogrom etc), or simply organically, by virtue of the location and culture where the religion is "growing".
So after not too many decades you end up with variants of the religion - see the variants of Christianity for example: Catholicism and Orthodoxy split apart because of geopolitical considerations, dressed up as different interpretations of the religion; Protestantism and Catholicism similarly; North African Kopts on the other hand were separated (I think) mainly for reasons of local culture and distance from the rest. In Judaism you have the Sephardic (Spanish/Middle Eastern) and Ashkenazic (German/Eastern European) Jews. In Islam you have the Shias, the Sunnis, the Sufis and so on.
The tragic aspect of all this is that followers of each of the sects I mentioned (and the many I have missed out) each believe that they are the true believers, that only they have the absolute truth. And any depictions and icons etc linked to religions are culturally driven. It is no accident that the Christian "God" is traditionally shown as white and male, which is pathetic to say the least, when one considers that all major religions were founded by dark-skinned people!
So the differences and anomalies we observe today owe much to the cultural etc "impurities" acquired by religions, and are also influenced by our own personal cultural/religious prism, no matter how hard we might try to be objective. You yourself, in your opening post referred to "the obvious and ever-manifest hostility of Islam towards Judaism & Christianity", unwittingly ignoring the fact that the hostility goes both ways, and indeed the hostility between Shias and Sunnis (for example) is stronger than the one between them and Jews.
A good comparative religion course will try to shed the extraneous influences and compare the basic tenets of religions - and will find many similarities between them, unsurprisingly. It sounds like you have benefited from one such course. But it will not explain the hostility engendered - to do that one has to take the extraneous "impurities" into consideration.