And yet the article shows the original sketches Wright made for the building that show the asymmetrical H's with the bars aligned with the bars on the E's (i.e on the upper half) in virtually identical font to what was eventually installed.

I don't really see how you can come away with the conclusion that this suggests lack of intent; at most, it seems like you had already formed the opinion that there was no intent, and you didn't find the evidence to the contrary convincing enough that you were wrong. I don't think your take is necessarily wrong, but I don't think it's fair to characterize the evidence as suggesting what you're saying.