Its not so much that backup managers need the syscalls for peek and poke, its that they use peek and poke to add other syscalls. The syscalls in question (35 and 36) have to be in lv2 and modifying lv2 will cause the ps3 to crash. The reason it works in 3.41 was because of the lack of protection against it.
3.55 introduces the checksuming (of some kind we really aren't sure what they are doing) to lv2 at runtime and routinely checks to make sure that it remains the same. We need to find where this is being called and remove it obviously but that takes time. Also, since most modifications to lv2 crash a ps3 using peek and poke, the only way to do it is to modify it at runtime using a pup. But, using a pup brings in the risk of permanently bricking the ps3 so most don't want to go down that path.