How would the Government obtain similar information if the person under criminal investigation (SBF) was not using Google and was using his own mail server instead.

For those worried about privacy, consider that Google may be a far greater concern than the Government. Unlike the Government, (1) Google is not subject to one hundred plus years of case law enforcing laws to protect citizens from unwarranted government search and seizure and (2) Google's business is invading privacy and collecting data about people. The Government, unlike Google, is not making billions of dollars by surveilling computer users; it does not depend on unregulated online privacy invasion and unconstrained online advertising.

The Government does even need probable cause to ask for pen register data from Google (cf. seizing a person's personal mail server which would likely require warrant). Another argument not to let Google collect and store peoples' data.