Borders still affect the positioning of things even with box-sizing set to border-box. For example, here "Block 1" is still two pixels taller than "Block 2":
Does that really matter though? A difference of 2px for something temporary doesn't seem like much concern. While I understand the implication is that these can accumulate and cause larger layout issues, the purpose of this practice is to highlight those areas to remove that accumulation anyway
I have never wanted anything other than this behaviour, so I pretty much always include it when starting on a fresh project.