MSN has both .com and index.html

[AnthonySE]

Make sure all links point to the home page and not the index.html.

yourdomain.com NOT yourdomain.com/index.html

[bluesky]

Don't worry. all websites have both their homepage and index.html or htm or php or other extensions copies.

Yes, pointing the links to your main address is better & can help in boosting PR as well.