Civil operators pay money because they can make more money; they don't fly into Darwin/Williamtown/Townsville to make a loss!
As for..
If the military want their own systems they can pay for it out of their own budget and have the benefit of Military only zones.
They
do pay for it from their own budget! And it's why, when they were built, military bases were generally where no other operator wanted to be; it also resulted in the benefit of their own CTZs.
If it weren't for the 'can do' attitude and compromise by military personnel to do their best (always more with less!) acceding to the lobbying and political pressure for civil access,
every military flying base would be safer
without civil traffic in the mix.
Finally, as for 'perpetual training', it's what tends to be necessary when an organisation's under-resourced/limited ATC staff do duties in Iraq/Afghanistan/disaster zones etc for long periods,
and at their home base. All at the behest of a grateful nation.