In my case, here is the solution (maybe someone needs a reference applying what @armstrove said):

# models.py

class PagexElement(models.Model):
    """Smallest reusable building block for page construction. Elements contain HTML templates with placeholders that can be customized when used in pages. One or more elements compose a section."""
    ...

class PagexSection(models.Model):
    """Collection of elements that form a reusable section. Sections are composed of one or more elements and define the structure for page layouts."""
    ...

class PagexInterSectElem(models.Model):
    """Intermediary model to handle the ordering of elements within a section. Allows the same element to appear in different positions across sections."""
    ...
    class Meta:
        unique_together = [["section", "element", "order"]]

# admin.py

from adminsortable2.admin import SortableAdminBase, SortableInlineAdminMixin
from django.contrib import admin
from . import forms, models
...

class PagexInterSectElemInline(SortableInlineAdminMixin, admin.TabularInline):
    model = models.PagexInterSectElem
    formset = forms.PagexInterSectElemFormSet
    ...

@admin.register(models.PagexSection)
class PagexSectionAdmin(SortableAdminBase, admin.ModelAdmin):
    """Customizes the management of layout sections."""
    ...

# forms.py

from adminsortable2 import admin
from django import forms
...

class PagexInterSectElemFormSet(admin.CustomInlineFormSet, forms.BaseInlineFormSet):
    """Custom formset that allows duplicate elements in different section positions."""

    def validate_unique(self):
        # Skip the default unique validation for 'element' field! Pagex only cares about section+order uniqueness (handled by DB constraint)!
        super().validate_unique()

    def _validate_unique_for_date_fields(self):
        # Override to prevent element uniqueness validation!
        pass

Cheers.