The next thing that comes assuming they ever get operational will be students with no time on type being sent of on consolidation flights without an Instructor as is planned and banging one in. Mark my words.....
I doubt there will be anyone, let alone students, flying consolidation flights with no time on type! Or was that another poorly worded post where you meant low time?
The Phenom is not a pocket rocket, it's a relatively simple - certainly very easy to fly - small twin. The transition from the Prefect to the Phenom will be very straightforward and far easier when compared to previous airframe changes such as: Chipmunk-JP, JP-Hawk, Gazelle-Wessex to name but a few.
If you want a pilot who can only operate within quite a narrow environment (take off, transit, land), stay well clear of any limits, operate rigidly iaw very restrictive SOPs then perhaps the civilian CPL type course is the way to go. However, if you want a pilot who needs to be able to fly perhaps at LL, air-air refuelling, para drop, ISTAR or tanking to the absolute limit of your endurance, as part of a multi-aircraft package, with aircrews from other nations and using very different SOPs, to the extremes of your aircraft's accepted limits, then I would argue the CPL route doesn't work. You need a pilot that's had exposure to various skills - including basic formation - and most certainly on a few carefully considered sorties 'solo' ie without an instructor on board.
I've seen both systems close up, each have their pros and cons; but please don't think that sending a pair of well trained students, thoroughly briefed, on a well planned local sortie is unwise. It's an essential part of the military pilots' training and confidence building.