Is there a difference in insurance coverage when booking cars through Priceline/Hotwire, rather than booking directly on the rental company's website?

To give a precise answer you will have to compare the fine print of both insurance policies and those will likely be different from car rental company to company and website to website.

However indicatively I found the following to be the case:

• Protection: It is possible that the insurance of the rental company covers car parts that are not covered by most secondary insurance policies (i.e. priceline/hotwire or insurance provided by your credit card). An example would be the seats and the motor I was once told.
• Refund in case of accident: likely in the case of an accident with the cheaper policy you would first have to pay your excess to the rental company and then claim that payment from your secondary insurance. See this question (and also the excellent answers) for an example of this and this answer in a related post that is worth a read. Instead the rental company insurance would cover the excess immediately without you needing to step in and then reclaim your money, which could take a while.

Of course when picking up the car the agent will point out these differences and more or less aggressively try to sell you their insurance. If you can live with the above risks/disadvantages of your pre-purchased insurance (you might need a print-out as proof) then you are fine. If on the other hand you could never afford e.g. not having $1,200 for a year because secondary insurance is slow in paying you out, then the more expensive option might be in your favor to avoid risks.

But again, it all depends on the fine print, there is no general answer IMHO.