Here's what runs through my mind when thinking about it the two different option.
Side panels resting on Bottom panel:
This design is based strictly on the shear strength of the silicone bond as the outward pressure of the water will want to slide the side panel off of the bottom panel.
Sides resting on the stand:
This design is based on the tensile strength of the silicone bond as the two pieces would be effectively forced apart. There would theoretically be no shear force involved as the side panel would be resting on the stand exactly as the bottom panel.
So, this comes to a debate of shear strength vs tensile strength;
I just did a quick Google Search to find this Info. As noted below, the tensile strength is much higher than the shear/tear strength. So, from a simplistic idea, it would be better to have the panes on the outside rather than sitting on top of the bottom pane. One reason that companies may do this is it makes the tank easier to assemble inside the plastic frames.
****Note - This is just a random silicone that came up. Not necessarily for aquarium use.****
http://www.dcproducts.com.au/RTV_Silicone_Solutions/Tech_Data_Sheets/RTV120S-tds.pdf
Side panels resting on Bottom panel:
This design is based strictly on the shear strength of the silicone bond as the outward pressure of the water will want to slide the side panel off of the bottom panel.
Sides resting on the stand:
This design is based on the tensile strength of the silicone bond as the two pieces would be effectively forced apart. There would theoretically be no shear force involved as the side panel would be resting on the stand exactly as the bottom panel.
So, this comes to a debate of shear strength vs tensile strength;
I just did a quick Google Search to find this Info. As noted below, the tensile strength is much higher than the shear/tear strength. So, from a simplistic idea, it would be better to have the panes on the outside rather than sitting on top of the bottom pane. One reason that companies may do this is it makes the tank easier to assemble inside the plastic frames.
****Note - This is just a random silicone that came up. Not necessarily for aquarium use.****
http://www.dcproducts.com.au/RTV_Silicone_Solutions/Tech_Data_Sheets/RTV120S-tds.pdf