The problem isn't to do with the separator at all, this is only an issue if you were inserting the formula into PHPExcel directly as
=ZÄHLENWENNS(Migration_LSA!$AR$2:$AR$121;">=1/4/2014";Migration_LSA!$AR$2:$AR$121;"<=30/4/2014")
when you would need to set the locale, and use the translate methods before inserting it. Internally (in both PHPExcel and MS Excel) formulae are represented in their English/US format. The MS Excel GUI hides this from you with automatic translation on insert/display.
At the moment, the COUNTIFS() formula in PHPExcel only works with a single range/criteria pair.
You can work round this by splitting your multiple range/criteria pairs into single range/criteria pairs and adding those together, so:
=COUNTIFS(Migration_LSA!$AR$2:$AR$121,">=1/4/2014") +
COUNTIFS(Migration_LSA!$AR$2:$AR$121,"<=30/4/2014")
setReadDataOnly(true)
tells the PHPExcel Reader only to read the cell content, not to read styles, format masks, print settings, conditional styles, etc... but formulae are still cell content