Clarification of parameters for HaplotypeCaller

Hi I'm new to GATK and am looking into using HaplotypeCaller to call chloroplast variants in a plant. I am interested in both the variant sites and invariant sites in my sample (relative to my reference).

I know that in order to get confidence in homozygous reference sites, I should use:

--emit-ref-confidence BP_RESOLUTION 

But how does this differ from

--output-mode EMIT_ALL_CONFIDENT_SITES

?

Also can someone please clarify the difference between

--base-quality-score-threshold

and

--min-base-quality-score? 

Many thanks!

PS I am also looking into Mutect2 for calling chloroplast variation but am not quite convinced that a somatic caller is what I want here so for now would just like to understand HaplotypeCaller better. Thanks!