That means if i upload my days work using go-ipfs, then i upload those same files to ntf.storage as backup copies, i won’t be able to access the ntf.storage “version” if my node is offline. Is that correct?
Yes you cannot, different CID == different files as far as IPFS is concerned.
You should upload .car instead. (they are archive of IPFS blocks so instead of web3.storage rechunking and rehashing your files, web3.storage is just gonna store the exact same block that your home node produced)
You can export a .car from your node with ipfs dag export Qmfoo > example.car