I'm following the idea of the example from the fromJSON documentation that sets a JSON matrix in one job, and passes it to the next job using an output.

The first job collects the true and false values from the inputs and creates a JSON object with key-value pairs where key is the repo and value is the boolean value. jq removes the elements with false and creates an JSON array of the remaining keys. This is put into the outputs.repos variable for the next job.

name: repos
on:
  workflow_dispatch:
    inputs:
      repo_1:
        type: boolean
        default: false
        description: Use Repo 1?
      repo_2:
        type: boolean
        default: false
        description: Use Repo 2?
      repo_3:
        type: boolean
        default: false
        description: Use Repo 3?
jobs:
  job1:
    runs-on: ubuntu-latest
    outputs:
      repos: ${{ steps.step1.outputs.repos }}
    steps:
      - id: step1
        run: >
          echo '{
            "repo_1": ${{ github.event.inputs.repo_1 }},
            "repo_2": ${{ github.event.inputs.repo_2 }},
            "repo_3": ${{ github.event.inputs.repo_3 }}
          }' 
          | echo "repos=$( jq -c 'map_values(. // empty) | keys' )"
          >> $GITHUB_OUTPUT      
  job2:
    needs: job1
    runs-on: ubuntu-latest
    strategy:
      matrix:
        repo: ${{ fromJSON(needs.job1.outputs.repos) }}
    steps:
      - run: echo ${{ matrix.repo }}