Bluetooth: chip or module?
Let's start with the bottom line: What is the total price difference between the IC solution and the module solution (Taking only the CC2541 vs. the RN42)? This turns the question into a balance between NRE and BOM spending. 

Using optimistic numbers for your sales, let's look at prices per unit at 1k volume. I'm going to use the manufacturer's 1k prices. This gives us a better price per part, but really this is well suited for spreadsheet analysis:


RN42: $11.72 per unit at 1k quantity, $117,200 extended cost (RN42-I/RM630)
CC2541: $1.59 per unit at 1k quantity, $15,900 extended cost


This gives us a naive budget difference of over $100,000 for making 1,000 devices. The question you must ask yourself is "will developing for the CC2541 cost me less than $101,100?*"

(*) Insert your actual pricing numbers.

Note that your margin shrinks rapidly as you sell fewer and fewer units, or the closer the two are in price. Overestimate your sales volumes and you may have spent a bunch of time and money that you couldn't afford in order to develop a cheaper solution that not enough people want.

If I take the Digikey timeline figure at face value and pay one to two people to work on this at $50k/year, that puts labor costs between $50k and $150k, but quite possibly more. Don't forget to pay yourself! Don't forget that they qualified their statement with


  If your team has sufficient RF expertise and the software skills...


How long do you think it would take to get the module working? Probably not nearly as long as the IC, but the product development may still be months.

Keep in mind that there are additional costs to the CC2541 besides just a longer development cycle. You may have more hardware revisions due to difficulties with the antenna system. You will need FCC certification, which will be more expensive for the IC. There are many variables. Assume that it will be harder than you thought, and will take longer than you thought, especially if you are unfamiliar with the technology.

Given these numbers, below 1,000 units I would probably stick with the module.