I believe in the situation describes, the tabernacle (containing the consecrated host) remains the center of attention and you should genuflect towards that location. In ours, the altar sits directly in front of the tabernacle.
Why not discuss with the priest why it’s arranged like that…sounds like moving the tabernacle or the altar would be an easy fix.
For less than 1% of churches, there may be a reason. St. Peter’s in Rome has a constant flow of tourists taking pictures and exploring the specific art and architecture of the main altar. The Blessed Sacrament is reserved in the Adoration chapel which is still very much part of the church itself. That particular church, and few others, is so large that the normal rules of making the Blessed Sacrament prominent, or the center of orientation, do not apply.
In one church downtown, they have adoration many hours a day (except when there is Mass). The Blessed Sacrament is reserved at a prominent side altar to the left of the main altar, but still in the front. This way people praying in adoration are much closer to the Blessed Sacrament than if it were in the middle, main original altar which is some distance back from the congregation. But the prayerful orientation in that Church is always to the front. There** is **a front.
Catholic churches in “the West” have historically been oriented towards “the East”, longing for Christ’s return. Of course, in many cases the building has been shaped by the realities of the real estate available, so “the East” does not have to be literal. But there should be a “front” to the church. The crucifix, the altar, and the Blessed Sacrament should be visible in the same glance. They are related! I am willing to bet your church keeps the bible in a prominent position, not in a back closet. That’s appropriate, but you might want to ask why appropriate…
When the Blessed Sacrament and the crucifix are removed, the center of attention becomes the priest, the choir, and other things. Sometimes bad architecture lingers because no one takes the initiative to talk to other people about a change.
In 1978 a document by a committee of bishops, “Art and Environment in Catholic Worship” helped influence the design or redesign of buildings, like your church. But that document was totally superseded by a 2000 document, “Built on Living Stones” which is now the authoritative guide. But many churches are still influenced by the outdated document.