Order Management does not support the inclusion of optional service items in a configured Model BOM (see Support article #1296751.1 for more detail). Allowing for such would therefore require customization.
As you've found, there's no modeling restriction that prevents you from creating a Model BOM that includes optional service items, nor is there any problem with creating a Configurator Model for it. And required service items (such as a warranty item that is a required child of an optional BOM component) do not present a problem; they have nothing to do with Configurator, and would never appear as sub-lines in OM. The problem arises in OM, which requires that any service item be "associated" to the item it's "servicing". OM does not automatically make such an association with service sub-lines, even though it might be argued that an association may be inferred by the BOM structure (i.e., OM does not assume that an optional service sub-line is necessarily associated, from a service standpoint, with its BOM parent). OM customization is therefore required in order to hook any service item up to its corresponding product item. Many customers who configure service along with product have implemented such a customization.
(Another gap in such a solution that may be relevant to you is that for an included optional service item requiring recurring billing, Order Management does not create the requisite Service Contract. Customers have likewise developed customizations to address this, as well.)
As this is not specifically a Configurator matter (you could have created your order without using Configurator at all, and you would have experienced the exact same behavior), please do not take my explanation as being either authoritative or comprehensive (I am a Configurator expert, and only knowledgeable enough about Order Management to be dangerous). It would be advisable for you to seek more detailed information/recommendations from the Order Management forum.