Here is my understanding of your question and then the solution I propose.
You have to produce 1700 maps always about a given region (the island shown in screenshot).
In this maps theres is two_layer
black circle in layer_a for every plant species distribution 2000-2019
grey square in layer_b for every plant species distribution 1975-1999
I do not really understand the structure of your data sets.
You have posted your "coverage" layer - seems ok for me.
I understood, that you have two shape files with points for dispersion of your plant species. Is this correct?
I Think, you must have a layer with the squares covering your area of interest.
Now for your problem:
If I understand it ...