Ahh...good old calculated Items.
I am not sure if this is possible if these items are all in the same column (sum of amount). You might need to bit the bullet and format as "#,###.00" - so percents are decimals less than one.
You can try getting this into a table format rather than a report format...that could give you more options for formatting columns of data. This may not be possible in your situation.
Another solution is to custom format the cells, not the pivot fields -- see below.
It might also be possible to have two sum of amount columns to work on...again, maybe this is not feasible in your situation.
Sometimes Pivot Table are good for the crunching and the final report format for presentation is outside the Pivot Table, or on another sheet.
Basically, as far as pivot tables go, if you can do it in Excel you can do it in Excel VBA. So if you can get this to work in a native interface, you could macro the same steps. There won't be any special properties or methods you can use in VBA to do what you can't do in native Excel.
Sample sub:
Format cells (using regular cell properties, not pivot table properties. I've been lazy with the formats as anything not a number or a percent is hidden...you might need to clean this up. Who knows what it would do to text. And, of course, anything that looks like a percent will be formatted as one. Also, sometimes to select pivot table cells you need to "navigate into" the table with arrow keys and the shift key.
Code:
Sub myFormats()
Dim c As Range
For Each c In Selection
If c.Value < 1 And c.Value > 0 Then
c.NumberFormat = "0.00%;;"
Else: c.NumberFormat = "$#,##0_);[Red]($#,##0);"
End If
Next c
End Sub