Published fares will generally be non commissionable to a TA so they are not making a dime on these fares by selling them to you. £1000 air fare will go 100% to the airline. This is why a lot of travel agents will add on a ticketing/servicing fee on top.
BT/IT fares (aka private/consolidated fares) will have a lower net fare (say £920 on the same route) and the TA will generally mark up the sell price to be slightly lower than the published offering (say £990) in order to be competitive. Being a competitive sales environment, TA's will generally encourage their agents to promote these fares first in order to generate revenue for their business. Avios and tier points given (given it is a BA flight) will be the same. I know DL has other ideas about this.
Rules and restrictions may be different so in the same guise it is important to incorporate your needs from a FQTV scheme into the total equation when deciding what fare to use. You would tell a TA you need flexibility, you should also tell them your plans for upgrading using points so that they can advise the most appropriate fare to you. I don't think it's fair to point the finger of blame entirely at your TA if you haven't been completely up front to them in the first place with regards to your intentions. In fairness it probably just didn't occur to you as it wouldn't to many. Just put it down to experience and remember for next time.