There was some discussion at SES Denver about the importance of consistency in phone numbers relative to Local. The context was pay-per-call and the dynamic numbers used in that scheme. Practices exists that will enable publishing differing phone numbers without disrupting structured data, but that's not my point.
There was some uncertainty about the role the number plays in data cohesiveness. Personally, I feel it's the glue that holds everything together. When we speak about atomization, I think it's the phone number that binds those atoms into a critical mass. I'm not debating the merits of pay-per-call, but I am interested in hear from those in the know -- is not the phone number the common thread that holds the tapestry together?
The phone number is one prime element used for matching listings up between systems. For instance, if you were a hotel site, Google Local might use your phone number as one element to match up your website with reviews of your business found on other sites.
Obviously, other matching criteria can be used as well, such as street address, but there are situations where phone number will be used/trusted more such as for businesses in malls or shopping centers or in big office buildings -- all of which have many businesses sharing the same street addresses.
So, using special tracking numbers mostly impacts the abilities of directory sites to properly aggregate your data with their various data sources.
I don't really think it would hurt traffic to your online biz information, nor overall referrals to your business.