Hi @Sharuk
Thank you for posting.
According to your description, you have several concerns related to shared mailbox with different domains.
First of all, as long as you have verified all these different domains within your O365 tenant. The mentioned accounts are all internal accounts even though they has different suffix names.
It looks like they are all located your O365 tenant. So you have 3 different domains verified in your O365 tenant.
Target mailbox: sapemail@r1p.contoso.com
Source shared mailboxes: abc@ite.contoso.com & xyz@contoso.com
Flow owner : svc@contoso.com
1.how to configure a flow for the mentioned email ids (abc@ite.contoso.com & xyz@contoso.com) can both of them can be configured under contoso.com or it has to be configured under ite.contoso.com?
We should create two flow for each of them as this trigger can only be applied to one individual shared mailbox. Since the flow owner is <svc@contoso.com>, we should assign full-access permission of these two shared accounts to svc account in advance.

https://docs.microsoft.com/en-us/connectors/office365/#when-a-new-email-arrives-in-a-shared-mailbox-(v2)
https://docs.microsoft.com/en-us/exchange/recipients-in-exchange-online/manage-permissions-for-recipients
2.somewhere I heard, it is not possible to access ite.contoso.com using contoso.com since svc@contoso.com is not the part of ite.contoso.com! is it correct ?
No. Actually, the access capability has nothing to do with domain suffix. As long as <contoso.com> has full access permission of <ite.contoso.com>, it’s definitely possible to access. One more thing needs to pay attention is user mailbox can access user mailbox as well as shared mailbox no matter what is its domain name. However, it’s recommend use shared mailbox to access another shared mailbox.
3.I'm thinking write some info into SharePoint lists, if both (abc@ite.contoso.com & xyz@contoso.com) are different then we have to create 2 different SharePoint sites and 2 different flows for each in ite.contoso.com and contoso.com ?
Yes, but it’s not because they have different domains but due to they are two different accounts.
4.can flow is capable to forward the emails to 1 domain to another domain ? i.e. abc@ite.contoso.com (shared mailbox in ite environment) to sapemail@r1p.contoso.com (sap mail in r1p contoso.com)
Yes, it’s absolutely possible. Here is how flow is configured.

Hope the content above may help you.
Best regards,
Anna