Let me summarize some correct facts prior to answering your question:

• Vitamin D is indeed lipid-soluble vitamin, therefore it is only comes in capsules with oil or in liposomal form.
• Absorption under the tongue (sublingual absorption) is amazing for water-soluble medications, however works for lipids in lipisomal forms too.
• Any fat soluble vitamin can cause overdose in large quantities (unlike water-soluble), however therapeutic window for vitamins usually is pretty large. Therapeutic window is the dose range that can be safely taken without significant risk of overdose. Specifically for vitamin D, your recommended daily dose varies between 1000U and 5000U (depends on the season, place of living and your ethnicity). For severe deficiency we can prescribe 50000U weekly for a couple months. To overdose you need to take much more - more than 10000U daily for a few weeks.

Now to direct answer to your question - you are not missing a lot:

1. Yes with no optimal sublingual administration, absorption could differ. Bu it is not a chemotherapy, it is vitamin D - difference in health benefits if absorption dosages slightly inconsistent is minimal.
2. Whatever was not absorbed sublingually will be absorbed later in your GI tract.

Basically, don’t overthink it. And try not to ask health advice from internet strangers, better talk with your primary doctor if you have any concerns.