Yes, you're definitely over-thinking it. Beefheart himself said to just experience the album and let it sink into your brain subconsciously.
However, I could say rather bluntly and superficially that there was absolutely nothing like Trout Mask Replica before and after its release in not only rock music, but music in general. He completely changed the idioms in which he worked with, and since you're trying to appreciate his work... it's best to consider the time period. (Although, I still find his work incredibly ahead of its time... even today).
There's a saying that goes something like... "It takes about six or seven listens to Trout Mask Replica until you begin to enjoy it." It really only took me two, but I've found that the former is more common.
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