I believe Johnny is paying a full trust on his new employer, as he doesn't want to leave a bad image at the first place. Further more, HR thingy is very complicated sometimes, and it is fine for him to pay in advance.

I can imagine if Johnny insist not to pay in advance for Apple, his reputation and image will soon drop to the bottom. Offending the employer before stepping into his new office, he is indeed digging a grave for himself; In opposite, the former employer may also insist him to do a clearance before he can leave the company. In such dilemma, I truly understand Johnny has no choice but to trust his new employer, since a reputable company is highly likely won't decline to what they had promised to Johnny earlier. The only "out of expectation" is the tax and epf deduction of the reimbursement.

In my experience, Apple should issue the reimbursement to Johnny in a separate form. It can be cheque, cash or bank account credit same like salary, but not together in the monthly salary transaction. HR's payroll system will calculate tax and epf deduction automatically. This is the exact situation/problem which Johnny has met with. As such, such reimbursement has to be handled individually.

As a conclusion, this was a mistake by HR personnel. Not sure what is the best mitigation on this, but for sure it will create a lot of issues and troublesome. Payment made is hardly to be refunded especially from government agencies, such as KWSP and LHDN.

Please correct me if I am wrong, I believe HR needs to send a letter to LHDN to inform of the mistake of reimbursement payment recorded as taxable allowance. HR will then need to get a notification or agreement from LHDN, to allow them to file the document as evidence and followed by modifying some entries in payroll system. In the year-end EA form, the relevant payment should be reflected as reimbursement instead of allowance. And then, Johnny should proceed to claim for "Cukai Terlebih Bayar" in the subsequent year of tax submission. As for KWSP, no turning back as I do not come across any case whereby KWSP "refund" any payment to either employee or employer.

** No offense, solely my personal opinion in a possible mitigation. May not be the actual solution, so do comment to correct me as i may wrong.