Well... Given the fact that Skill Versatility allows you to choose Perception and another skill, rather than only Percepton from Keen Senses, there's really no reason to use that variant. The fact that it's presented as an option is likely an error that has yet to be errata'd. If you truly want to force only one skill proficiency instead of two, you could either homebrew this particular half-elf variant, or else just choose Perception in Skill Versatility and leave the second option blank.

Ah! Okay. Well, it's important to note that subrace is not the same as variant, and all of these half-elf variants are built assuming that choosing them means you're replacing Skill Versatility according to the "Variant Half-Elf" rules in SCAG. So for example, if you look at the other half-elf variants, they are already missing the Skill Versatility trait, and instead have either been replaced with the new feature that the variant grants. Or in the case of the variants with more than one option, a generic "Half-Elf Variant" trait that grants options to select from.

If you were to create a variant race where one feature replaces another, you'd start by creating the variant race and ensuring "Is Variant?" is checked:

... and then creating the feature, setting the feature type to Granted, and having it replace the intended base race racial trait:

There are also a number of ways you could represent this functionality in a homebrew race without actually using variants. Following in the vein of the options to select from for the "Half-Elf Variant" trait for both high half-elves and wood half-elves, you could create a trait in a base race that also offers options to select from.

Another way, which I haven't tested other that giving Customize Your Origin ASIs, languages, and skills to my homebrew races but which theoretically should work, is to create optional replacement features. Under Feature Type, you'd choose Replacement (rather than Granted), and then select the appropriate feature to replace under Racial Traits to Replace.