This is Moira from the Social Care team at Shopify. Thanks for posting, and a very warm welcome to the Community!
Without looking at your store, it is difficult to pinpoint why your sitemap is not showing on your homepage. If you were to reply with your store URL, I could take a closer look at your domain's root directory, but for now, I will give you some general troubleshooting feedback.
Before you submit your sitemap, you need to verify your domain with Google Search Console to confirm that you're the owner of your Shopify store. If you don't already have a Google Search Console account, then you need to create an account. Follow these instructions to ensure you have verified your site properly.
A common reason why sitemaps don't appear is due to the storefront password. Sitemap readers can't access the sitemap when the password page is enabled. If you still have it enabled you can follow the steps here to disable the password. Once your sitemap is successfully submitted, the process of crawling and indexing your site can take time, and Google doesn't guarantee how long it'll take. You can learn more about what to expect from Google's Help Centre here.
You also mentioned that other issues are occurring because of this sitemap error, I'd be happy to look into this further if you provide all relevant information below.
Moira | Social Care @ Shopify
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This is probably the most common-sitemap issue that you will encounter in Google Search Console. This error message means that your sitemap has a page listed with a known crawl error, but the status of the error is unspecified.
Oh wow I'm surprised, that's something I never noticed! Probably because it's never caused any problems for any of the sites I've worked on.
How have you concluded that homepage URL not specified in sitemap is what's causing your site to not (yet) be indexed? How do you know it's not indexed?
To answer your question @themakeupgawd, there's no platform native way to edit the sitemap in Shopify. But there are ways like CloudFlare Workers modifying HTTP requests in transit. This is a rabbit-hole with some complexity (O2O, CF Worker Config) and costs (CloudFlare Business+ plan) attached, it's also non-standard meaning so no Shopify tech support. Also... it's likely to be a waste of time looking for a fix for something that is not a problem in the first place.
Your home page shows up all good in a site: search
Only 3 URLs showing, but including the home page, so likely the home page itself is likely 'indexed'. What does Google Search Console say for the home page URL index status?
I would try submitting your sitemap URL in GSC: https://themakeupgawd.com/sitemap.xml see what that does after a week or two.
Have seen it taking anywhere from days to months to get the site initially indexed - not sure how long your site has been live.