[dice]

[Why keep roots out of water reservoir]
It is not necessarily going to affect the plant negatively,
it is just that there is more risk of root disease in an anaerobic
environment than in a rooting medium with plenty of air space.
(Hydroponic setups may be different because of the fairly
constant movement of the water.)

A study I read on biocontrols for fusarium attacking geraniums
in greenhouses found (just by accident, not really what they
were looking for) that disease incidence was consistently
reduced in the container mix that had the most large pore
air space (they were using multiple commercial container
mixes), across all of the different biocontrols that they
tried as well as the uninoculated control plants.

(The reservoir in the bottom of a self-watering container is
rather severely lacking in large pore air space.)

Edit:
Some plants, bog plants and the like, would not care at all about
having roots in the water reservoir, that is their natural, hereditary
condition. That is perhaps not the case for tomatoes, though,
given how much trouble growers have with diseases that thrive
in wet soils and commonly infect the plant through damaged roots.