Inquiries about Monthly tax deductions and tax number

I started working on 25 June 2018. The company told me that 28% of my salary will be deducted each month till i become resident starting from Jan 2019 and that the difference (18%) will be refunded in April 2019. My basic salary is RM4000.

For the first month (June) i received salary without any deductions. I asked them about it they said that i don't have a tax number yet and that they will apply for a tax number for me and that i don't need to do anything.

In July i got my salary again without deductions. They told me at that point that my contract is for 1 year and that i am treated as a resident because i was hired in June and not July. They said expats who would be residents by Jan 2019 earning less than RM5000 per month can pay taxes for the period from June 2018 till December 2018 at one time at a resident rate during tax filing in April 2019. (instead of paying 28% each month and getting refund in April 2019). And that starting from Jan 2019 resident rate will be deducted monthly.

So,

1- Is that true? I mean can i choose to pay for that period at one time in April 2019 at a resident rate instead of paying 28% then get refund?

Till now i have been getting my salary without any deductions. I spoke with the HR and they told me that they already applied for a tax number for me and they will receive it soon. I went to LHDN and they told me that i don't have a tax number!!

2- Is there a fine for applying for tax number after 2 months? Also, is that the real reason there wasn't any deductions in my salary?

I am travelling from 21 Dec 2018 to 2 Jan 2019 (12 days) on a social visit.

3- Is there a problem travelling between 2 years, even if it's less than 14 days?

4- From what i said, Is there something i should do to prevent any future fines or penalties? I feel like my company is trying to hide something from me regarding tax. In many times they keep choosing what questions to answer and ignore the rest of my questions.