Lossless formats are gapless by definition and will be decoded as such by any competent player. Winamp fits that description.
Lossless formats are gapless by definition
Is it recommended to use CUERipper rather than EAC for ripping to individual flac tracks using FLACCL and preserving the gaps/no gaps, or is EAC just as capable?
EAC is just as capable.A notable difference is that CUETools automatically chooses the method for detecting gaps, whereas EAC allows manual selection among three different methods, defaulting to A, which should be fine for most drives. I see no reason why, given correct automatic detection in CUETools and the right manual choice in EAC, the two programs would not return identical results.
The audio will be exactly the same.The tags might change along the way due to something you do; we can’t speculate about that.
As you guessed, it shouldn’t matter at all. The audio should be decoded losslessly to WAV in any case before being re-encoded. The only exception would be if one or more of the decoder and encoder were broken, but then even that wouldn’t be affected by whether or not they were the same version, etc.