I am sorry, I couldn’t know about your background. Some users expect recipes for workflows they don’t yet understand and in these cases it is hard to help. This is why I mentioned the ESA materials.
The “subtract topographic phase” checkbox was only recently added and I haven’t tried it myself but I expect the results to be the same. It just combines two steps at once.
If you are working with Sentinel IW data, coregistration is a bit different, you at best use the TOPS Coregistration in the very first step where you can directly define the subswaths and bursts you need (as described here) which reduces a lot of time if you only need a smaller part of the image. But you have probably already seen this. For me, debusting after the interferogram formation worked best so I would agree to your second workflow.