Expariates in india - actual tax calculation

if the USD income was Bonus, Profit  Sharing or stock giveaway by a MNC to his employee in India, then will India tax still apply.

Also, if this expat is paying tax in his home country (assuming USA), then his mandatory deduction like social security and medicare--how will all that be treated?

It gets really involved !!!!

Section 5 read with section 9(1)(ii)  is very clear that all income (whatever may be the resident status) even if accrued outside India for services rendred in India, it is taxable,   bonus, etc payable overseas but for services rendered in India it is taxable in India.

The second part of your question is really technical, which is a bit difficult for me.  But to my small tax knowledge if status is Non Resident, then he has to pay tax in both the countries for the respective services rendred (ie) for services rendred for US business in US and for Indian business in India.  If RONR or Resident all income to be taxed in India for services rendred in India.

I hired Habibullah & Co. for tax services related Expat tax in india and surely they did the great work, I am mentioning them here because I really liked their work and wanted to give them a shoutout,

I recommend them and check them out once. 

https://www.hcoca.com/international-expat-tax-india.aspx