As with most NewGRFs, ISR will replace the stations of the default base set.
If by "compatible", are you asking if they work together? Yes, there are no technical conflicts between the two.
If by "compatible", are you asking if they look nice together? Absolutely not. ISR is 8 bpp hand-drawn graphics, zBase is 32 bpp machine drawn graphics.
Actually ISR does not replace the default stations. It is possible for a station NewGRF to replace the default station graphics, but to my knowledge, no station set actually uses this option - certainly none that I have used. Generally, the amount of possible station types is not small enough to be worth overwriting the default types for most authors - people generally like having the default ones even if they rarely use them.
The two cases where could think it would be preferable to overwrite the default station would be 1) a small OGFX+ type NewGRF with the purpose of making a small incremental improvement to the default station (such as retaining the default sprites but adding waiting people or cargo etc), or, 2) a set that finds the default stations are simply far, far, to incongruous in style from other graphics added. (However, in that case, it is likely that the rest of the base set will also look out of place. I feel this is one reason why 32bpp NewGRF development has sort of stalled - without a matching base set, a NewGRF that looks too different appears sort of out of place)