ArcGIS Pro Map Coordinate System for Models

[KansasDASC]

Running a multistep geoprocessing model using ModelBuilder in Pro 3.x. We have input raster data either in one of two coordinate systems. Part of the process is to clip the output of coord system 1 with a shapefile of counties set to coord system 1. When we run a raster file set to coord system 2, then we use a different county file for clipping that is set to coord system 2.

We are not displaying anything in the Pro project Map view, only using MB to run and output to a file directory. We're wondering about the Map coordinate system and if that has to change each time we switch the MB tools to use the data set to coord system 1 versus 2?

In other words, if we're running a model using data in one coordinate system, clipping with data set in that same system, but the Map coordinate system is in a different coordinate system, is that going to be an issue if we're only running a MB process? I couldn't find anything online to help understand this.

[ShitijMehta]

Please could you share a snapshot of your model?
In a model, are you setting the output coordinate system on the environments tab of a tool dialog?
if yes you can add a conditional check using the logical tool and then pass the correct coordinate  system. 

[curtvprice]

Here's an application of the conditional check Shitij is suggesting to use the county dataset you want based on the coordinate system of the input raster: