Ok so after getting the latest blockchain downloaded from the torrent without using any bootstrap file, just using all the files from the bitcoin data directory, no reindexing was needed. This means there is no need to make a portable version of the client and the bootstrap.dat files should not be used for the latest bitcoin clients as they don't include the index folder and other files. Using the bootstrap.dat would take much longer to sync and i am not sure if it is ever worth using a bootstrap file anymore, maybe if you are using older clients.