I just sed T/T to T here, you'll have to complete the sed expression with the other combinations.

$ bcftools query -f '[%CHROM:%POS\t%SAMPLE\t%TGT\n]' invcf.gz | sed 's%T/T$%T%' | datamash crosstab 1,2 unique 3

    S1  S2  S3  S4  S5
RF01:970    A/A A/A A/A A/A C/C
RF02:1726   T   T/G T/G T   T
RF02:251    A/A A/T A/T A/A A/A
RF02:578    G/G G/G G/G A/A G/G
RF02:877    T/A T   T   T   T
RF03:1221   C/C G/G G/G C/C C/C
RF03:1242   C/C C/C C/C A/A C/C
RF03:1688   T   T   T   T   G/G
RF03:1708   G/G G/G G/G G/G T
RF03:2150   T/A T   T   T   T
RF03:2201   G/G G/C G/C G/G G/G
RF03:2315   G/G G/C G/C G/C G/G
(...)