Retirement tax questions

The only reason why I'm not approving the answer is that I not sure it is correct, to be honest it doesn't make sense.

 

IRA balance : $1000 non deductible + $100 bonus.

 

While doing the conversion I pull out the money from IRA and already pay taxes for the $100 in my tax return. 1099-R shows $1100. 

At this point the entire amount was taxed and it goes directly to Roth IRA. 

 

Roth IRA receives $1100 and 5498 (box 3) shows $1100.  This is the only input that Roth IRA receives, every dollar in this amount was taxed. 

 

@dmertz @How is it possible to have $1,000 as basis and not considering the entire amount? The way I understand it, my contribution to Roth is $1100 and I can withdraw this entire amount without any split or headache