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The output does not follow the BED6 specification: "chrom, start, end, name, score, strand"

The first 3 output columns comply with the BED3 standard (chrom, start, end), but if strand is to be included, it should be in column 6. Column 4 should be name (we'll put the collapsed gene name list there), and column 5 a score (we'll put the region count there).

We can use awk to re-order the fields:

cat merged.good.sc_genes.txt | awk '
  BEGIN{FS=OFS="\t"}
  {print{ $1,$2,$3,$6,$5,$4}' > merged.good.sc_genes.bed