Institutional configs are not included when `NXF_OFFLINE` is on

Description of the bug

In the pipeline template, custom_config_base is set so that it will be downloaded from github automatically:
https://github.com/nf-core/tools/blob/34bc33802e8b51cadb62a3f0c615cf7a947100f6/nf_core/pipeline-template/nextflow.config#L63

As far as I understand, this is the reason this config is excluded later when running in offline mode:
https://github.com/nf-core/tools/blob/34bc33802e8b51cadb62a3f0c615cf7a947100f6/nf_core/pipeline-template/nextflow.config#L208

When downloading institutional profiles, nf-core/tools will set custom_config_base to"${projectDir}/../configs/", but nextflow will still ignore it when NXF_OFFLINE is on.

Either nf-core/tools should remove the conditional on L208 when downloading the institutional profiles, or this conditional should be adapted to include this file as long as custom_config_base does not point to github.

This is a follow up to https://github.com/nf-core/tools/issues/3132

How to reproduce:

• nf-core pipelines download demultiplex --download-configuration yes --compress none --revision 1.5.4 --container-system singularity
• export NXF_OFFLINE='true'
• nextflow run nf-core-demultiplex_1.5.4/1_5_4/main.nf -profile test,singularity,uppmax --outdir outdir

Command used and terminal output

N E X T F L O W   ~  version 24.10.3

Unknown configuration profile: 'uppmax'

System information

No response

Read nf_core/pipeline-template/nextflow.config around lines 63 and 208, then reproduce the issue with the provided nf-core pipelines download and offline nextflow commands. Check how the downloaded institutional profile is referenced when custom_config_base points to the local configs directory. Done means the uppmax profile is available and the offline run no longer reports it as unknown.