While it's possible I wouldn't cut 17mm in one pass has it will impact on finish and stress for tool, also risk of tearing the material depending on grain.
Quick Z level roughing won't take long with 6mm straight flute cutter and 3mm step which will greatly improve finish and work load for ball-nose finish cutter.

Regards tool change then your way of using shank length is asking for trouble and very unreliable. Bottoming the shank out in the spindle is bad for the spindle and it's bearings transferring heat and shock loads straight into it.

Presume because your not working off the material surface to reference new tool that you have chopped it away.? . . . In this case then you may find it easier to position your model in Cad so all moves will be in the positive direction and the bottom is at Zero in Z axis. This then means you can reference all tools off the bed and so long has you set enough rapid clearance height in Cam to clear material height you won't have a problem.

Another and far easier way if you use Mach is to setup a touch plate probe and use a screen set like Gerrys 2010. The CNC Woodworker - Mach3 2010

This has great feature for changing tools were after first initial touching off top of material it keeps track of the tool offsets and by touching off a fixed probe point it AUTO sets the tool height offsets for you and all you do is change the tool. Doesn't matter how far shank into spindle or tool length it does all the calcs and setting zero's etc.
You can even tell it where on the machine you want it to move too for changing the actual tool before it goes off and finds the new tool height.
If set up to do so it will start the spindle and carry on thru the code or wait for you to start spindle then carry on.

This combination of Fixed and moving probe plates means you can either very quickly manually set Z height off any point or like in this case were 3D model gets top surface cut away makes tool changes very easy and very accurate with the full Auto tool change.
Another Plus and great asset when used correctly and in conjunction with movable probe plate is the other probe options for things like finding centres of holes or circles, corners of parts, edges of parts, parallel edges etc