I have many opinions on this but I'll stick to just a few to not create a massive unreadable paragraph.
Servants and pets, rather than being disabled due to any magic use, should be disabled due to voidal magic use. There is precedent for that in machine spirits being weakened by the use of voidal magics. That and pets of any Tier aren't really 'bound' to the user unless you have an obedience module and thats not exactly soul magic. I don't know why magic being cast by the user should shut them off. Should have any magic cast in say, a 3x3 disables it instead of magic cast by the user.
Machine Spirits, you've seen roughly the same opinions from people above so I won't repeat those statements 1-1. Having a clear definition of what constitutes an actual dead & loss of a body is nice to have. I do have some qualms about the limit of 3 machine spirits only. If you are trying to make it more similar to klones you should realize how wildly different the two methods are. Klones are a much more time consuming method, you aren't going to be hopping bodies all the time considering the quality you can put into them without a MArt. Although they each last much longer. Machine Spirits on the other hand can be made in roughly a week at best or two without help. Though they are much more simple, you won't really get a bunch of 'mutations' put into each spirit so in exchange for quality you have quantity.
As it stands, wonderful formatting. Good to see some thought put into the process, but personally not a fan.