This was indeed intended. Not all settings are saved in the winboard.ini file. Some settings, likely to be one-time events, are exempted. This was already true in WinBoard 4.2.7, and applies for instance to the -variant option: you always start with normal Chess. It also applied to -firstChessProgram and -secondChessProgram: when not giving those on the command line (and not explicitly stating that you wanted to play without Chess programs) you would always get the startup dialog to ask for the Chess-program name(s), and never the same program as you used last time.
I considered the time odds something that typically depends on the engine you run, it makes little sense to give A time odds when it plays B with white, and in the next game B time odds when A has black. So I grouped it with the 'volatile' options. Normally such options would be passed to WinBoard by the Tournament Manager on a per-game basis. The 'WBopt' feature in the engine startup line can be used for this without the TM being even aware that it happens (so that it should work with any TM).
Note that there is a case where I am in doubt: there is a group of settings which has a default value which makes it dependent on other options. For instance -boardHeight and -boardWidth. The default (-1), means basically that there is no default, but that the setting varies according to what is default for the selected variant. (So in normal Chess you get an 8x8 board, in xiangqi you get 9x10, etc.) These options almost never have to be used, but I do save their settings in the winboard.ini. Perhaps this is a mistake; if you ever used them to play, say, Capablanca Chess on an 10x10 board (rather than the normal 10x8), the next time you start WinBoard you would start in normal Chess, (as the -variant was not saved), but with a 10x10 board! The options can be changed through the menu. though, so it is not disastrous. But perhaps it should be better to not save settings that are expected to be dependent on other settings that are also not saved.
Note that you can see in
this list which (new) options are supposed to be saved, and which not, in the current version: the saved options are marked with an asterisk.