I do not play Wargods, but the same question can be asked for any rules set, regardless of period or genre.
Mostly it is personal preference. Personally, I prefer rectangular bases as it eliminates most arguments as to whether an attack is frontal/flank/rear, because the sharp corners clearly define the partitions. It alleviates a lot of hard feelings, and arguments, in my experience.
I also find rectangular bases easier to use for tighter, shoulder-to-shoulder formations of troops, versus irregular formation, where the troops do not fight shoulder-to-shoulder. It helps everyone line them up, on the table, in neater, more defined units. Again, personal preference.
I also believe it is easier to make rectangular movement trays. compared to round base movement trays, as I do not need to cut out a bunch of circles, I just make rectangles, with edging on the outside; the bases, themselves, help hold the stands in their proper positions within the movement trays. Just my two centavos. Cheers!