I think I'm missing something here. I would think if the torque spec is the same, it wouldn't matter a bit if you went with different bolts as it's the registers that locate the caps. The bolts just provide clamping force. Or is the thinking that increasing the torque would slightly collapse the caps, leading to an egg-shaped condition? I would hesitate to increase the torque on the main caps because a bolt is only good as what it's threaded into and cast iron is not the best material for a threaded application.
The big factor is breakaway torque, which is more influenced by what lube you use on the threads. It is also influenced on a new bolt by how many times you have torqued it.
I agree with Jay in that if you don't torque it more than before it should be ok. ARP likes you to use their lube, so if you were using motor oil with stock bolt, that might make a difference.
I would use the same lube with the ARP bolts and I think you would be ok. The only real way to know is to measure it though.
I had a friend with a 289 that bought aluminum heads, so he also bought Ford Motorsports head bolts. When he assembled the engine he use some kind of moly lubricant instead of oil and torqued the heads down. He kept snapping head bolts until he realized the moly lube significantly changes the torqued required on the head bolt. Break away torque is more significant than most people realize.
For instance the last time I retorqued my head bolts, I marked the head bolts with a marker to see how far they moved. First I just retorqued them after a day and none moved.
Then I loosened them before retorqueing and they all moved about the same. I think if you're going to retorque the last torque has to be at least 30 ft lbs or so or the bolt won't overcome the breakaway torque. Same thing with initial torque, for those who torque in 10 lb increments, I doubt the bolt is being torqued to final spec.