Not arguing, I'm not a roofer, but why can't they be nailed to the rafters over shingles, there are nails and screws as long as you want and it would seem simple to locate the first rafter and measure from there, checking occasionally on the inside to make sure you're on target. What am I missing?
When installing the purlins, you want them as solid as possible. They go horizontally across the rafters and need to be attached directly to the rafters. If you attach them to the sheeting, they can work their way loose over time. A metal roof should last fifty years, so there is a lot of time, weather and movement that has to be taken into consideration.
I'm not saying it's impossible to hit a rafter every time, especially once you figure out where they are and measure it out on every purlin. It's just that the odds of a crew doing it every time are pretty slim.
The second problem is that the shingles are uneven and allow for future movement. This is assuming that there is only one layer of shingles on the roof. If there is more then one layer, it's just going to be that much more uneven. Then there is the length of the fastener. Are you using full 3 inch nails or screws? An inch and a half through the purlin, half an inch through the shingle, half an inch through the decking only leaves half an inch of nail going into your rafter. That's not going to hold anything in place for very long. I would want as much going into the rafter as I could get. With impact drivers and 3 inch screws, I know I can get that screw counter sunk half an inch into the wood and have half the screw or more into the rafter.
Last reason to remove the shingles is to inspect the decking. What has been going on up there and is there any damage? Valleys and areas around vents are famous for leaks and damage. How does the decking look? I absolutely hate to cover up a problem and if I'm spending the money for a high quality roof that is going to last the rest of my life, I am going to do everything I can to make sure it's going to last as long as possible.
In my line of work, I've found that the additional time and expense in materials is insignificant to the overall scope of the job. Cutting corners to save time or a buck always ends up costing more in the long run. While I'm not a roofer, I do enough repairs to roofs to see a pattern in why they fail.
Eddie