Quinn Glass built the plant at the former Ince Power station site near Elton without waiting for approval of a planning application submitted in July 2004.
And ahead of a crunch 16-day public inquiry starting on Tuesday, at which 500 jobs could be on the line, the firm has submitted a list of alterations made during construction.
They include a new staff car park, the enlargement of a loading and lorry parking area and the removal of some landscape planting.
A separate application to Ellesmere Port and Neston Borough Council seeks retrospective permission for a helipad, which will be considered by planners independent of the inquiry.
But the changes have further angered opponents of the scheme.
Scott Rowlands, of Mimosa Close, Elton, said: 'It's disgusting - no normal person would get away with this. Money talks at the end of the day.'
Mr Rowlands claimed HGVs were now using residential roads 'as a racetrack', adding that he also feared pollution from the plant.
Eric Davies, of Redwood Drive, Elton, said: 'I am appalled the development has been allowed to reach the stage it already has without planning permission being given.'
A report by Chester City Council planning officer, Brian Hughes, said many of the changes were 'extremely minor', affecting the external fabric of the buildings.
He admitted the new parking area and enlarged lorry parking and loading zone would bring vehicles closer to houses in Station Road and Ince Orchards, but said acoustic measures would limit the impact.
Mr Hughes told councillors English Nature had raised concerns over the possible harmful effects of the helipad on nesting birds and protected ecological areas.
But he said: 'None of the changes, with the exception of the helipad, are likely to have any harmful impacts. There is no reason why the council should not support these changes at the forthcoming inquiry.'
Councillors agreed to express concern that information supporting the helipad, including a revised environmental statement, did not appear to identify all the potential effects of the development. But the board concluded 'that it does not consider that the changes will have any additional material impacts on the appearance of the development, the character of the area.'
Quinn Glass declined to comment.
The crucial public inquiry begins at the Queen Hotel, City Road, Chester, on Tuesday.
An evening session has been arranged for residents from 6.30pm on December 8 at Elton Community Centre, School Lane.
Following a challenge by Quinn's rivals, Rockware Glass, a High Court judge last month said the decision to invest millions in building the plant without planning permission, had been a 'very considerable gamble'.
Judge Andrew Gilbart QC also condemned Chester City Council's 'unacceptable and lax' approach before it issued a Pollution Prevention and Control (PPC) Permit for the plant in March, a decision he overturned.
He said chief executive Paul Durham had 'acted outside the scope of his authority' in issuing the permit, which enabled the first of the plant's 600-tonne furnaces to be 'fired up'.
The judge granted Quinn permission to appeal against parts of his ruling and 'stayed' the quashing order pending the outcome of an Appeal Court hearing.