TC has a partial embedded focus, not changing the kernel from under users has benefits. Anything from no new regressions to not invalidating custom kernel modules. Upgrades of Core are supposed to be safe and easily applicable.
Of course TC will work with custom kernels just fine, in case you require 4.1 or any other such version. If you run a security-conscious service, such as a public server, you should consider RHEL/CentOS.