Yes, of course. See Question A-2 (arc42 License).
Completely free to use and modify
You may modify the structure of the template, re-create it in any tool of your choice or even rename it for your own purpose (one of our clients called it SAT42, what we really enjoyed.)
To be fair, you should reference Gernot Starke and Peter Hruschka as creators of arc42 in case you use or modify the template…
Internal customization never has to be published
You can copy, modify and use arc42 inside your organization without ever publishing anything. The ShareAlike condition applies when you make an adapted version of the template available outside your organization. Whatever you change for your own teams stays yours.
Your own content is not affected either. The license covers the template, meaning its structure, its headings and its explanatory text. What you write into it belongs to you and follows your own rules.
If you distribute, you need to respect the CC license
If you distribute such derivations or enhancements, for example on your website, in a public repository or as part of a product you ship, you need to comply with the (very liberal) Creative-Commons Sharealike 4.0 license, which allows you to:
- Share: copy and redistribute the material in any medium or format
- Adapt: remix, transform, and build upon the material for any purpose, even commercially.

arc42 is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.