(1) At the moment, there is no way to replace boot.ini, unless the $OEM$ folder has such a function to place a file in the root of your drive.
(2) INI files cannot be slipstreamed. If you want to put it in a certain folder, read about it
here, but keep in mind, only the folders listed are supported for HFEXPERT.
(3) Hotfixes using the /Q switch (Type 2) still belong in HF.
(4) The ISO name is defined under ISONAME in HFANSWER.INI. You should be able to enter a path there, but paths aren't really a "supported" feature, so make sure you know what you're defining.