There are no battim made completely by hand - all battim makers use high-power presses to form the leather into shape. All tefilin need to be made lishma anyway therefore humans are required in the process. The difference lies in who/what powers the machine that sands down the battim, as explained by NoachmiFrankfurt in his answer.
R Reuvain Mendlowitz in his book Inside Stam explicitly asks the question (p. 145)
What is the difference between factory-made battim and privately-made battim?
- Private battim means that one individual toils for many, many hours on each and every step involved in creating a pair of battim.
The process is not rushed, all halachic requirements are fulfilled,
and - most importantly - unwavering attention to detail is expended
- The goal of the producer of factory-made battim, on the other hand, is to produce the maximum number of battim in the minimum
amount of time. This goal is achieved by having a different person
doing each job, somewhat similar to an assembly line. While this
system dramatically decreases the amount of time necessary to produce
a pair of battim, it does, nevertheless have its drawbacks.
He then goes to list the drawbacks:
- the reliability of workers (how experienced are they?, how well
trained are they?, how well do they know the halachot?)
- attention to detail: a private battim maker treats each product with full attention, care and takes whatever time is necessary to craft a perfect product
- halachic standards: in many factories, various halachic leniencies are relied upon, particularly in the creation of the shin on both sides of the shel rosh. Although thes battim are certainly kosher, the might not be mehudar.
He concludes by saying that, of course, this does not mean that every private battim maker produces battim that are of superior quality or of a higher halachic standard than those produced in factories. But, in general, a reliable, honest, privater battim maker will produce a mehudar product while at a factory this is not always the case.
He also advises, throughout the book, to ask for a hechsher (certification) on the important parts of the tefilin: battim, retzuot and of course parshiot.
See also here for a related answer.