But when we look at life on a biochemical/molecular level, the analogy with engineering strengthens, rather than weakens. ...
No. As an engineer, a designer, and a partial micro-biologist (courses taken but no degree), and as the son of a biology professor that I often discussed such things with (before he passed), I can definitively say that this is wrong.
There are two things engineers employ that contradict this assertion:
1. KISS -- Keep It Simple Stupid -- means no frills or "spandrels" that don't add to the structure or the function. Think of a bicycle in it's simplest form. Nothing that is not needed.
2. Cost-Benefit Analysis -- to ensure the design is cost efficient with little or no wasted time or material.
So when I "drill down" to the microbiological level I see waste, and over complication, and more of the impression of systems pieced together ad hoc, jury-rigged to accomplish tasks with little control on timing.
This is a rather shoddy argument, ...
The cell design is rather shoddy and make-do, rather than engineered, with a lot of duplication of effort.
... Paley's argument was that life "looks designed," and therefore was designed (by agency). ...
Which, as you should know, is a logical fallacy. A → B does not mean B → A.