This comes down to choosing the right tool for the job. Perhaps their application is written using frameworks which enable/enforce this kind of normal transactional processing of requests.
Now if the existing application is the only way that they know how to get to the data, then it may easily become the golden-hammer / silver bullet that gets used for performing an upgrade, rather than writing an external sql script which they might not be familiar with. Add to this the common convention of "nothing touches my database except my application", which has proven to be useful by preventing rogue updates which cause application 'bugs', and the golden-hammer / silver bullet becomes even more appealing.
SQL script wouldn't be the only non-application choice, there are quite a few good ETL solutions available, however these tend to cost quite a bit and perhaps the vendor does not want to impose another licence fee onto the client.
This brings up a point more relevent to the main article thread, when deciding whether to throw people or hardware ata particular problem, you always have to be aware of the hidden costs i.e. licences for all software used including pre-requisites, network capacity, server-room capacity power & cooling etc.
Naturally wide-spread use of open source software makes the initial calculation of software licencing cost a lot easier, although I'm sure that there are those who could argue that the savings on open-source software licences are eroded by necessary additional staff costs.