Are there any alternatives to Liftoff

Hi,

I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1: bioconda installation); however, it only picked up gene features from the reference GFF3 file. Reference GFF3 file contains many features, including CDS, mRNA, etc.
Command I used liftoff -g SALTOL_Nip.gff -o BG94_1.gff3 BG94_1.fasta SALTOL_Nip.fasta
My original GFF3 file looks like follows;

##gff-version 3
##source-version geneious 2021.2.2
##sequence-region   SALTOL  1   5800001
SALTOL  Geneious    source  1   5800001 .   +   .   Name=source Oryza sativa Japonica Group
SALTOL  Geneious    misc_feature    1   1   .   +   .   Name=misc
SALTOL  Geneious    misc_feature    2   100001  .   +   .   Name=misc
SALTOL  Geneious    misc_feature    100002  200001  .   +   .   Name=misc
SALTOL  Geneious    gene    1   1349    .   +   .   Name=Os01g0293800 gene
SALTOL  Geneious    gene    114140  118531  .   -   .   Name=Os01g0295900 gene
SALTOL  Geneious    gene    105528  108078  .   -   .   Name=Os01g0295700 gene
SALTOL  Geneious    gene    102152  104528  .   -   .   Name=Os01g0295600 gene

and output I am getting is;

Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    1   1345    .   +   .   ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0
Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    1623    3128    .   -   .   ID=gene_6;Name=Os01g0293900 gene;coverage=0.999;sequence_ID=0.968;extra_copy_number=0;copy_num_ID=gene_6_0
Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    20379   21605   .   -   .   ID=gene_7;Name=Os01g0294500 gene;coverage=0.999;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_7_0
Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    48673   50214   .   -   .   ID=gene_5;Name=Os01g0294700 gene;coverage=1.0;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_5_0
Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    102125  104501  .   -   .   ID=gene_4;Name=Os01g0295600 gene;coverage=1.0;sequence_ID=0.992;extra_copy_number=0;copy_num_ID=gene_4_0

I raised the issue at GitHub a few days back and still waiting for an answer.
Are there any other tools you folks recommend for this purpose?
Thanks in advance!