fix: remove SR --replace_rg that strips PL:ILLUMINA from short reads

The modular hybrid pipelines applied --replace_rg to SR reads in pass1,
mapq0_bed, and stage3 rules, replacing their original read group (which
includes PL:ILLUMINA) with a minimal RG lacking platform info.

The Sentieon hybrid model uses PL:ILLUMINA to identify short reads.
Without it, SR data was invisible to variant calling (SAD=0,0 for all
variants), producing identical results regardless of SR coverage depth.

The CLI version never applies --replace_rg to SR reads. This fix matches
that behavior. SR reads keep their original RG from sr_align (which
already has the correct SM tag), only LR reads get --replace_rg with LR:1.

Fixes: HIOM-MOD and HIPBM-MOD identical concordance for different SR
coverage levels (e.g. SR5x vs SR20x both showing F=0.8468).
