Hi,
Intune and SCCM are two products, so it may not related to M365 E3 licenses of Intune.
About how to get it, we could refer to this link from Microsoft:
https://learn.microsoft.com/en-us/mem/configmgr/core/understand/product-and-licensing-faq#what-do-the-acronyms--sa--and--l-sa--mean-in-regard-to-configuration-manager-
Way to buy:
https://www.microsoft.com/en-sg/Licensing/licensing-programs/licensing-programs?rtc=1
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