Seems like a difficult task. There is another option for reworking BGA's and that is to print solder paste on top of the BGA balls (see "BGA and QFN Repair Process" APEX 2008). The stencil gaskets to the balls and gives a very uniform solder volume.

Based on the information that you have provided, you are stenciling onto the PCB. In this case you would want to do an inspection of the site as the Micro Stencil can become misaligned, the stencil can be accidently placed onto an adjacent part or the operator can miss-wipe the squeegee causing voids.

If you were using a Stencil Print Plate that prints the solder paste onto the solder balls, you would have much higher success rates with your printing applications and not have to tie up your inspection system.

Sense can mean different things to different people. The criticality of solder paste height increases as the size of the BGA increases. So, for a 600+ I/O BGA, I might answer that knowing solder paste height is important.

If the BGA is only 256 I/O, then maybe a simple visual inspection might be sufficient. The risks involved are also critical.

How expensive is the BGA or the product?
How many times can you rework?

Answers to these questions should help you determine if solder paste height inspection is necessary and cost-effective.

Note: When I audit EMS providers, I tend to aggressively push for solder height inspection for all products of medium to high complexity.