这个问题我也遇到了，因为自定义主题是需要将scss加载进来的，而scss中引用的字体不能被对应的loader正常解析（猜测是这个原因），而将element自己便于好的css使用js模块引入就没问题。
应该还是scss编译机制的问题，目前虽然没有找到具体原因，但是已经解决，方法如下：
1. 注释
element-variables.scss
// @import "~element-ui/packages/theme-chalk/src/index.scss";
2. 新增
然后将elementui编译好的icon.css单独用js进行引入加载，即可解决，以下是完整代码：
//这里写你的自定义主题变量配置
$--color-primary:#4b6eef;
//将入口文件的引用拆出来引用到这里
@import "~element-ui/packages/theme-chalk/src/pagination.scss";
@import "~element-ui/packages/theme-chalk/src/dialog.scss";
@import "~element-ui/packages/theme-chalk/src/autocomplete.scss";
@import "~element-ui/packages/theme-chalk/src/dropdown.scss";
@import "~element-ui/packages/theme-chalk/src/dropdown-menu.scss";
@import "~element-ui/packages/theme-chalk/src/dropdown-item.scss";
@import "~element-ui/packages/theme-chalk/src/menu.scss";
@import "~element-ui/packages/theme-chalk/src/submenu.scss";
@import "~element-ui/packages/theme-chalk/src/menu-item.scss";
@import "~element-ui/packages/theme-chalk/src/menu-item-group.scss";
@import "~element-ui/packages/theme-chalk/src/input.scss";
@import "~element-ui/packages/theme-chalk/src/input-number.scss";
@import "~element-ui/packages/theme-chalk/src/radio.scss";
@import "~element-ui/packages/theme-chalk/src/radio-group.scss";
@import "~element-ui/packages/theme-chalk/src/radio-button.scss";
@import "~element-ui/packages/theme-chalk/src/checkbox.scss";
@import "~element-ui/packages/theme-chalk/src/checkbox-button.scss";
@import "~element-ui/packages/theme-chalk/src/checkbox-group.scss";
@import "~element-ui/packages/theme-chalk/src/switch.scss";
@import "~element-ui/packages/theme-chalk/src/select.scss";
@import "~element-ui/packages/theme-chalk/src/button.scss";
@import "~element-ui/packages/theme-chalk/src/button-group.scss";
@import "~element-ui/packages/theme-chalk/src/table.scss";
@import "~element-ui/packages/theme-chalk/src/table-column.scss";
@import "~element-ui/packages/theme-chalk/src/date-picker.scss";
@import "~element-ui/packages/theme-chalk/src/time-select.scss";
@import "~element-ui/packages/theme-chalk/src/time-picker.scss";
@import "~element-ui/packages/theme-chalk/src/popover.scss";
@import "~element-ui/packages/theme-chalk/src/tooltip.scss";
@import "~element-ui/packages/theme-chalk/src/message-box.scss";
@import "~element-ui/packages/theme-chalk/src/breadcrumb.scss";
@import "~element-ui/packages/theme-chalk/src/breadcrumb-item.scss";
@import "~element-ui/packages/theme-chalk/src/form.scss";
@import "~element-ui/packages/theme-chalk/src/form-item.scss";
@import "~element-ui/packages/theme-chalk/src/tabs.scss";
@import "~element-ui/packages/theme-chalk/src/tab-pane.scss";
@import "~element-ui/packages/theme-chalk/src/tag.scss";
@import "~element-ui/packages/theme-chalk/src/tree.scss";
@import "~element-ui/packages/theme-chalk/src/alert.scss";
@import "~element-ui/packages/theme-chalk/src/notification.scss";
@import "~element-ui/packages/theme-chalk/src/slider.scss";
@import "~element-ui/packages/theme-chalk/src/loading.scss";
@import "~element-ui/packages/theme-chalk/src/row.scss";
@import "~element-ui/packages/theme-chalk/src/col.scss";
@import "~element-ui/packages/theme-chalk/src/upload.scss";
@import "~element-ui/packages/theme-chalk/src/progress.scss";
@import "~element-ui/packages/theme-chalk/src/spinner.scss";
@import "~element-ui/packages/theme-chalk/src/message.scss";
@import "~element-ui/packages/theme-chalk/src/badge.scss";
@import "~element-ui/packages/theme-chalk/src/card.scss";
@import "~element-ui/packages/theme-chalk/src/rate.scss";
@import "~element-ui/packages/theme-chalk/src/steps.scss";
@import "~element-ui/packages/theme-chalk/src/step.scss";
@import "~element-ui/packages/theme-chalk/src/carousel.scss";
@import "~element-ui/packages/theme-chalk/src/scrollbar.scss";
@import "~element-ui/packages/theme-chalk/src/carousel-item.scss";
@import "~element-ui/packages/theme-chalk/src/collapse.scss";
@import "~element-ui/packages/theme-chalk/src/collapse-item.scss";
@import "~element-ui/packages/theme-chalk/src/cascader.scss";
@import "~element-ui/packages/theme-chalk/src/color-picker.scss";
@import "~element-ui/packages/theme-chalk/src/transfer.scss";
@import "~element-ui/packages/theme-chalk/src/container.scss";
@import "~element-ui/packages/theme-chalk/src/header.scss";
@import "~element-ui/packages/theme-chalk/src/aside.scss";
@import "~element-ui/packages/theme-chalk/src/main.scss";
@import "~element-ui/packages/theme-chalk/src/footer.scss";
@import "~element-ui/packages/theme-chalk/src/timeline.scss";
@import "~element-ui/packages/theme-chalk/src/timeline-item.scss";
@import "~element-ui/packages/theme-chalk/src/link.scss";
@import "~element-ui/packages/theme-chalk/src/divider.scss";
@import "~element-ui/packages/theme-chalk/src/image.scss";
@import "~element-ui/packages/theme-chalk/src/calendar.scss";
@import "~element-ui/packages/theme-chalk/src/backtop.scss";
@import "~element-ui/packages/theme-chalk/src/infinite-scroll.scss";
@import "~element-ui/packages/theme-chalk/src/page-header.scss";
@import "~element-ui/packages/theme-chalk/src/cascader-panel.scss";
@import "~element-ui/packages/theme-chalk/src/avatar.scss";
@import "~element-ui/packages/theme-chalk/src/drawer.scss";
@import "~element-ui/packages/theme-chalk/src/popconfirm.scss";
3. main.js 新增
main.js
import 'element-ui/lib/theme-chalk/icon.css
是个笨办法，但是从浏览器控制台可以看到content可以正常加载了，实际测试也解决了问题，希望有帮助
