Sorry for the late reply.
I started doing this when I was fairly new to SC and decided to run Dragon Reborn anyway. The recon on st. 1 was insane and I heard that a lot of people had experienced a reduction in recon when they created a custom.
I didn’t really think more about it and created a DR st. 1 custom with just the core and deep sleep. This made the recon way more manageable and I decided to do the same for the following stages. So compared to the normal subs from the main store, I think you get the same content but with less recon.
Since then, I’ve followed this pattern on st. 1-3, when I’ve been running a 4 stage sub and then created st. 4 custom with more modules.
To be honest this has worked really well for me, but I also think that an argument could be made for including (some) of the modules you plan to use in st. 4 in the earlier stages.
I think that there are so many good modules in the Q store, that I would never use this method for a single stager - only for st. 1-3 of a multistage if I only intent to run each stage for 30 days.
Hope it helps - let me know if you have additional questions.