I used to work at a software company that created products to run mid to high-end credit unions. (Taking care of pretty much all software needs.) It was also rumored to serve as the inspiration for Office Space, though I would imagine this is a rumor at many companies.
1. "Initech hires computer programmers that "update bank software for the 2000 switch"" I'm pretty sure some adjustments were made and tests were performed, just like they were everywhere.
2. "Initech has access to "the credit union software"" The company I worked for had complete control of the code running on client systems.
3. "Initech has access to "the credit union mainframe"" Our clients would allow us to log on to their mainframe systems. Some clients would restrict what we could see, but most just let us see everything. At the time I worked there, many to most clients would keep a modem line available at all times that we could use to log in. Everything was logged, so if you changed something you would probably get caught, but you could do it.
4. 81
"Initech's accounting department notices when the money goes missing" The company I worked at wouldn't have had any reports like that, but the credit unions would generally do a nightly balancing and if something was off, we would CERTAINLY hear about it, usually even before business opening. (So the needed transactions could be reversed/fixed/etc) Having Initech notice probably makes the plot easier to follow, however.
5. "Initech has a "Corporate Accounts Payable" department (although at least one transcriber disagrees with me and thinks it's "Corporate Councils Payroll")" No idea here. I suspect this was required by the plot once you had Initech being the one that notices the money is missing.
6. "Initech has a "Logistics" department." Most any company can have one of these. The place I worked certainly had people working on logistics.
7. "Initech has engineers who lack people skills sufficient to interface directly with their customers." We did not work directly with customers, but this was less because of a lack of people skills and more because engineer time cost more than customer service time and most issues could be resolved without programmers getting involved. Often on-call situations resulted in programmers interacting directly with customers, however. 760