The same basic methods can be followed, but there is a fundamental difference in the prioritization of features / issues. A company has the ability to allocate their own resources and therefore can consider allocated costs to the consumer group (in terms of lost time or productivity) rather than to the producer group.
With exterior software, or with shrink-wrap, the influence on allocation of resources in the consumer group diminishes (virtually to zero with mass consumer products).
The cost of upgrades is also often reduced with inhouse software. The cost of support can also be shown to increase. This all plays an important role in the prioritization of project activities, which include testing and defect resolution.
So to answer your question. No. There is no difference in method, only in the variables used to control the method.
With in house software, the cost of fixing any bugs is not as expensive as fixing something that has been shipped to external customers.
As such, many companies use a less rigorous approach when testing in-house software. Maybe the cut some corners that they normally would not, maybe the don't pump load testing as much since they have an idea about the max loads expected, maybe they don't press as hard with the negative test cases.
Some assumptions may change also, like the knowledge of the end user may be greater for in-house software versus external products, where you really know don't much about the customers.
But as Ed mentioned previously, many of the same principals may apply for your product. It depends on what you and your company for the final details.