I am no expert, but I think phd study counts towards residence permit. Because you work as a "scientific researcher", which is a not temporary purpouse of stay. Here is the link to ind: https://ind.nl/en/work/Pages/Scientific-researcher.aspx

Here is the link specifying which is temporary and non-temporary purposes of stay: https://ind.nl/en/Pages/temporary-and-non-temporary-purposes-of-stay.aspx

I am no expert, but I think PhD study counts towards residence permit. Because you work as a "scientific researcher", which is a not temporary purpose of stay. Here is the link to IND.

Here is the link specifying what temporary and non-temporary purposes of stay are.