It depends on your needs and intended use. Do you plan to keep anything on the bike, in the proposed bag, when the bike is left unattended? If transporting valuables, do you feel like removing the waterproof bag and toting it with you every time you stop and leave the bike (to avoid possible theft)?
For me, it came down to security, ease of use, and waterproof. Those factors pointed to the luggage rack with top box. After getting over the initial thought of the $$ spent, I never regretted it.
Benefits of the box, in my view:
- quick attachment/removal
- ability to utilize on other/future bikes
- used boxes (good cond) available at 60-70% of new...see ebay
I'm frugal and it took me years to take the plunge and buy a top box. In all of the the accessories I've owned in nearly 30 years of street riding and 50+ bikes, a top box and good aftermarket seat are 2 of the best investments. When possible, I buy used. If/when you sell, you'll find that total cost was minimal-- meaning money spent isn't a lost cause. The accessories will retain a value and you can sell them later. Your "cost" will only be the difference for what you paid vs. the price of sold item.
I avoid side bags as they add too much width, on a daily basis, and require that much more space for the bike when storing it in the garage. I haven't used a waterproof bag, as security of top box trumps the lower cost bag. If only using the bag to tote lunch/personal items to work, and take it with me when I go in, I might consider a bag for that. But, would not leave a bag on the bike (unattended) if it contained valuables: GPS, phone, laptop, camera, etc...