Hi,
In a tracker-program where you compose modules by replaying sampled waveforms, the common way to create samples of chords was to do a sample of the whole chord and all chords needed for creating the song. The reason for this was that the Commodore Amiga only had 4 channels 8-bit audio playback possibility by the "Paula" soundchip in that computer back in middle of 1980s. So, in the old days when the Tracker formats and SoundTracker/NoiseTracker/Protracker etc was publicly released to the masses, if you wanted to create a song and playback a chord, the best way would be to connect a "real" synthesizer/midikeyboard to your audio-sampler hardware and then sample the audio-output from that hardware sound-device of a chord. That would mean you needed to create and make a sample of every chord the song was in need for. Each chord sample would then only takes 1 audiochannel for the playback. That would leave the other 3 audiochannels on the Commodore Amiga for other playback such as; drums, bass, lead sounds. Which was the common setup of soundstructure for songs composed on the Commodore Amiga.
When the PC came around in the mid 1990s, with new and better soundcard possiblities that allowed more audiochannels than was possible on the Amiga, it then made sense to stop sampling chords and instead only use one sample of the root keynote and playback that sample in the amount of audiochannels necessary for creating the chord itself. This became a preferred way to do it for example when Fasttracker 2 on PC got released to the public masses etc. By doing only one sound sample to create many type of chords, it would save a lot of memory.
So, to summarize: On the Commodore Amiga you would still need many audio samples for doing the variation of chords needed in the composition of songs. Every new chord spent in the song, would result usually in a new sample. But.... There is a "mathematical" way to avoid a new sample, and that is by changing the root note of the chord during sample playback. The most typical and most common samples of chords, I would say was C minor and C major. Those 2 chords could further be played with a F-root key and then you get a F-minor or F-major playback. If you used them as a G-root key, you get G-major or G-minor etc etc. So, by sampling a major and minor chords, you could make quite many chords out of only those two samples.
For composers that came from Commodore 64 and was known to create SID chips with Arpeggio chords, the mathematical way of looking on creating chords was "0-3-7" for a minor chord and "0-4-7" for a major chord. Basically, those numbers are the numbers of transpose you would need to shift from the root key in order to create the whole chord. This mathematical way of looking at a chord also means that it was very easy to use Minor and Major chords on Amiga to move these up and down and fit in different other chords playing along side the melody. For example, if you go from C major to A minor, that would be easily done with C 0-4-7 to A 0-3-7. But, you could also use E 0-3-8 instead of C 0-4-7. Or you could use C 0-4-9 instead of A 0-3-7 etc. Basically, you just need to move the root key inside a chord and use the next combination that fits in the scale to move up or down in a chord structure.
So, by using that mathematical solution, sometimes the C-major and C-minor chords was not the optimal chords to sample. Because, when you had to shift them too far in different root-keys, the sound quality of the chord would suffer. For example, if the C minor is played at C-3 key, and then afterwards E-2 key, thats last chord sample will sound very "low quality" due the fact that the original sample was done in C-3 key. Therefore, maybe was it better to sample instead a G-2 Minor sample that played first at F-3 and then G#2. Both which would give same result as the first C minor played at C-3 and E-2.
Ok, that was a lot of technical stuff in regards of why Chords was sampled the way they where. And also why the chord progression often was a selection of best-efforts in how to make it sound good as the root-key was shifted during the song progress. This might sound very puzzling to you, but I hope it make more sense now when you read all the above and it would answer your question nr.2.
For question nr 1, I would still say that a C-3 Minor and Major chord samples was the most common way to use. There was also some "jazzy" versions of these, C minor7 is very often used in Amiga songs with more jazzy flavour to it. Also that chord can be played back in very many root keys and still one chord sample sounds okay in the mathematical way I explained above to fit the chord structures.
So, hopefully, my answers above together with the explaination made you any wiser - or more confused.

/Cheers Magnar