Can you try the below code?

• Include the field in search

SearchClient.Instance.Convention.ForInstancesOf<YourPageType>().IncludeField(x => x.SearchHitUrl);

• And then apply filter

var domainFilter= domainFilter.And(x => x.SearchHitUrl.MatchCaseInsensitive(keys));

To summarize the issue, the search hit URL must be part of the filtering that goes into the search before it is executed.  I don't know if that creates a problem with how the search works but I'm not aware of other options to search across a multi site setup.  It should be easier to filter based on the URL of the search hit.  I don't see a clear way to implement a multi site

@Sanjay, indexing the field makes sense but the instance type is ISearchContent.  Is that the preferred approach?

This is the exact initializer code I was able to use:

SearchClient.Instance.Conventions.ForInstancesOf<ISearchContent>().IncludeField(x => x.SearchHitUrl);

I reran the find index job and results are still site specific when using the domain filter.  I suspect the search hit URL is still not being indexed because it seems like it is more of an output than an input to filter on.

The way I am trying to filter the results by domain:

var domainFilter = searchClient.BuildFilter<ISearchContent>();
domainFilter = domainFilter.Or(x => x.SearchHitUrl.Prefix(SiteDefinition.Current.SiteUrl.AbsoluteUri)); // Include current site results

if (currentSite == SiteName.A)
{
  domainFilter = domainFilter.Or(x => x.SearchHitUrl.Contains("siteBdomain.com").Match(true)); // Include other site results
}

var query = querySearch
...
  .Filter(domainFilter)
...

If I understand correctly you want to create a filter to get search results of the current site in a multi-site setup. You have one search index and multiple websites

The following code snippet might able to help you

I'm filtering results based on the Current start page Ancestors

private IMultiSearch<IContentData> BuildMultiSearch(string searchTerm, int maxResults, int currentPage, int cacheResultsForMinutes,
            bool ignoreDefaultOperator = false, BestBetsResults bestBets = null)
        {
            var search = _findClient.Search<IContentData>();
            var useAndAsDefaultOperator = false;
            var startPageContentLink = SiteDefinition.Current.StartPage;
            if (startPageContentLink != null && startPageContentLink.ID > 0)
            {
                var startPage = _contentLoader.Get<StartPage>(startPageContentLink);
                useAndAsDefaultOperator = startPage.UseAndAsDefaultOperator;
            }

            if (startPageContentLink != null)
            {
                search = search.Filter(x =>
                    ((IContent)x).Ancestors().Match(startPageContentLink
                        .ToReferenceWithoutVersion().ToString()));
            }

           .......

Antoher option is to use .FilterOnCurrentSite() to get domain specific results

So we actually have 3 sites. We want to share the results from 2 sites between each other and have site 3s results be entirely its own pages. So site A and B both get A and B pages, and site C gets C pages only. I was sucessfully using a filter builder with an or filter(x => x.prefix("https://MySite1URL") or filter(x => x.prefix("https://MySite2URL") but we need a solution that will work across environments and multiple domains. We need it to filter on the urls automatically, if that makes sense? 

You can create a Filter method that applies a Filter based on parameter. 

Have you tried using Grouping filters?

Something like 

.Filter(x => (((PageData)x).ExternalURL.Match("site1url")) | ((PageData)x).ExternalURL.Match("site1url"))
//or
.Filter(x => (((PageData)x).ExternalURL.Prefix("site1url")) | ((PageData)x).ExternalURL.Prefix("site1url"))

Have not tried in solution but logically it should work. 

You can also do a match on the SiteId. Take a look at

https://world.episerver.com/documentation/developer-guides/search-navigation/Integration/cms-integration/Querying-examples/

The last example is the following:

var content = SearchClient.Instance.Search<IContent>()
  .Filter(x => x.SiteId().Match("MySiteId"))
  .GetContentResult();

I haven't used this, but it might should accomplsh what you are after.