elem-inst-test

elem-inst-test.bemjson.js

({
    block : 'page',
    title : 'elem-inst-test',
    styles : [{ elem : 'css', url : 'elem-inst-test.min.css' }],
    scripts : [{ elem : 'js', url : 'elem-inst-test.min.js' }],
    content : [
        {
            block : 'elem-inst-test',
            js : true,
            mods : { mod : true },
            content : [
                {
                    elem : 'elem1',
                    content : [
                        {
                            block : 'input',
                            mix : { block : 'elem-inst-test', elem : 'elem2', mods : { type : 'input' } }
                        }
                    ]
                }
            ]
        }
    ]
})

elem-inst-test.browser.js

// block
modules.define('elem-inst-test', ['i-bem__dom', 'objects'], function(provide, BEMDOM, objects) {

    provide(BEMDOM.decl(this.name, {
        onSetMod : {
            'js' : {
                'inited' : function() {
                    console.log('@root      _js_inited, self.getName(): ', this.__self.getName());
                    console.log('@root      elem1.value', this.elemInstance('elem1').value);
                    console.log('@root      elem2.value', this.elemInstance('elem2').value);
                    console.log('@root      .value', this.value);
                }
            }
        }
    }));

});

// block__elem1
modules.define('elem-inst-test', function(provide, Block) {

    provide(Block.decl({ block : this.name, elem : 'elem1' }, {
        onSetMod : {
            'js' : {
                'inited' : function() {
                    console.log('@__elem1   _js_inited, self.getName(): ', this.__self.getName());
                    console.log('@__elem1   .block().value: ', this.block().value);
                    console.log('@__elem1   .value: ', this.value);
                }
            }
        },
        value : '!!!!!!! it\'s elem1!'
    }));

});

// block__elem2
modules.define('elem-inst-test', function(provide, Block) {

    provide(Block.decl({ block : this.name, elem : 'elem2' }, {
        onSetMod : {
            'js' : {
                'inited' : function() {
                    console.log('@__elem2   _js_inited, self.getName(): ', this.__self.getName());
                    console.log('@__elem2   .block().value: ', this.block().value);
                    console.log('@__elem2   .value: ', this.value);
                }
            }
        }
    }));

});

elem-inst-test.deps.js

({
    mustDeps : {
        block : 'i-bem',
        elems : [{ name : 'dom', mods : ['elem-instances'] }]
    },
    shouldDeps : [
        'objects'
    ]
})

output

console.log:
@root      _js_inited, self.getName():  elem-inst-test
@__elem1   _js_inited, self.getName():  elem-inst-test__elem1
@__elem1   .block().value:  undefined
@__elem1   .value:  !!!!!!! it's elem1!
@root      elem1.value !!!!!!! it's elem1!
@__elem2   _js_inited, self.getName():  elem-inst-test__elem2
@__elem2   .block().value:  undefined
@__elem2   .value:  !!!!!!! it's elem1!
@root      elem2.value !!!!!!! it's elem1!
@root      .value undefined

No, you shouldn't. When you declare modifier of block or element, you get the same BEM-entity with additional behavior. When you declare element, you get another BEM-entity. I agree that this moment is unclear. This problem will be solved in bem-core@v3 where all elements are BEM-entities.