I would only do this if you are very short on space, which really is not a factor since 2 smaller tubs fit in the space of one larger tub.
The drawback on one tub for 2 clutches is that unless they are close in hatch date is that the media will not last much longer than 70 days or so without starting to mold if your humidity is 98%+ where it should be.
If one clutch pips much sooner than the first you will probably get pretty funky smelling in the tub from all the fluid when the hatchlings pip out. No matter how air tight your incubator is some bugs will find their way in there with that smell of rotting egg fluid left behind.
Out of 17 clutches last season, we only had 2 clutches where the lid would not close in a 6qt Sterilite tub with the eggs stacked. Just be careful and you can get them apart with dental floss, or a razor blade and a very steady hand
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