The constraint may have been knowledge. They may have made a very reasonable tradeoff to forego learning "best practices" and "proper architecture" to just get something out the door. The original developer may have just graduated with his philosophy degree and never have written more than a bash script. Hard to say.

Given the size of the company, the architecture didn't grow along org charts (that is a very real phenomenon in large companies!). Rather, the org chart grew along architectural lines. Regardless of cause, it is a pretty significant smell and can tell you something is (or will be) wrong.