There is only one advantage of having a built-in phono and that is, it
saves space, one less box. However if you are looking for the ultimate
sound you will find a quality external phono head amp is the only way to
go if you're serious about good sound! Here is another thing, if you
are not using the internal phono preamp, do not remove the tubes from
the circuit for safe keeping as this will damage the phono circuit.
I don't find this to be the case. The problem is the connectivity- if the phono section is built-in you don't have a connectivity issue. But if its external you do, which means the cable has to do a pretty good job.
You can certainly install a first class phono section in a preamp. Its all a matter of design; that preamp should be easily capable of keeping up with an external unit. What matters is not whether the phono preamp is internal or external so much as the intentions of the designer.