Why would that be so difficult? They seem to manage it pretty easily with staff wages.
My company also pays my expense reimbursements into a different account than my salary without any apparent issues.
Yes its not a massive issue but would be differing levels of work to differing companies depending how they setup their systems.
What typically works with a decent size payroll system is :
It contains records of employee bank details so knows where to pay the net amount from (and would normally generate an electronic file for process via some means). Then the other entries, NI, tax, student loans, pension etc would not be paid directly from the payroll system but would be on the balance sheet of the company and another mechanism would pay each one. Normally far more manual.
IF every person was allowed to have their salary deducted pension paid into what ever scheme they wanted then logically payroll software would adopt to allow this as extra details.
Some of the complexity comes also in that the pension providers oftern have their own system in place, portals, specifically formatted files etc, so they are not the same to deal with as a bank where you can simply send a BACs payment and the funds will be creditted to the correct account.
Nothing is insurmountable and code can be changed to cater for this but its not out of the box deliverable.
Lots of differing ways that expense can be processed so it depends on your employer typically. Those that pay via they payroll software don't/can't typically offer payment to a different account, those that have a dedicated piece of software or who use the accounts payable system tend to be able to accomodate a different account as the systems tend to be unlinked. I worked for one financial company that went from not allowing a different one, to allowing it back to not allowing again.
As they developed and evolved the systems flows (ie data between systems) was optimised for lowest manual effort. The end state was that the only employee data was collected and maintained in the HR system by HR and fed the data to relevant systems as required, e.g. bank details to the expenses processing system was a weekly feed that updated any changed records, in the background with no manual intervention.