You can set up 'sell the excess intermediates' on a ware by ware basis.
There's a 'sell/buy/both/none' button on each of the ware rows,
eg if you say 'sell ore', then the util assumes you've got a transporter
doing the selling and adjusts the profits (etc) calculation (and the
simulation flow) to suit. Its worth a quick look at the help doc
I think the reason why in-game intermediates build up, when the sheet/util
says it's exactly 100% of need, is due to dynamics, not a miscalculation.
This is especially true for long cycle time end-product complexes
(eg bHEPT). This is down to fast cycle wares (intermediates) 'stealing'
shared inputs wares (eg energy) from the slow cycle wares.
The extreme situation is gPPC, where in fact you probably need to add
as extra SPP to your complex to have sufficient (dynamic) energy stock
to keep the gPPCs producing.