The meaning is quite similar, but you'd usually translate בי as "in me" and בתוכי as "inside me". (the word תוך means the inside of something).
Times when this sentence could be used: "איפו בקבוקים של יין?!" Guilty looks... "זה בתוכנו" Or possibly: "Where has our youth and beauty gone, old friend?" Eyes tearing up "זה בתוכנו" But, yeah, it's probably an alien parasite.
Can you say what this sentence would relate to? What exactly is "inside us"? that would help me understand how and why you say it this way :) thanks