Possibly, but if you have lots of evidence under one offence (the same evidence that would have been spread over numerous offences) then I would think that this actually makes your one offence stronger as you only need to prove one bit of evidence to prove the offence. I would presume that the judge or magistrates can then look at all of the evidence in that offence and decide on an appropriate fine accordingly. The more serious cases with large multi nationals would probably end up in Crown Court anyway where the Judge can impose an unlimited fine.
I have had a successful case in the past where the defendant pleaded guilty to five offences (all 32(1)(a) involving articles 8, 9, 13, 14). In handing out the fine, the Judge gave a fine for Articles 8 and 9 and didn't give anything for the other offences, even though he had been found guilty.