You are correct, in your case the flights and accommodation are two separate issues.
The automatic requirement for filing passport details is essentially a USA initiated one, brought in after 11.9.2001. In my experience, when flying internationally within Schengen (EEA except UK and Ireland) it is not a requirement to log passport or ID details or on domestic flights, but it is anywhere else - in fact you cannot even board a flight to the USA unless you also possess a visa (one version of which is an ESTA). UK and Eire nationals additionally have to go through immigration in both directions when travelling anywhere to/from their countries (by ferry, air or whatever) whereas within Schengen no immigration facilities exist and all flights (Berlin-Rome, Paris Stockholm, etc., etc.) are treated as domestic. The Eire/UK situation is due to not being in Schengen and in the case of Eire the reason is the open border with the UK where no immigration facilities are maintained, else one suspects Eire would join the rest of restriction-free Europe in the Schengen Area.
It is a legal requirement in many countries worldwide to report to the authorities, or have available on file, passport or national ID details for all residents at hotels, etc.